Combinatorial polyketide libraries produced using a modular PKS gene cluster as scaffold

ABSTRACT

Combinatorial libraries of polyketides can be obtained by suitable manipulation of a host modular polyketide synthase gene cluster such as that which encodes the PKS for erythromycin. The combinatorial library is useful as a source of pharmaceutically active compounds. In addition, novel polyketides and antibiotics are prepared using this method.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. Ser. No. 08/846,247filed Apr. 30, 1997, now U.S. Pat. No. 6,391,594, which issued Jan. 27,1998 as U.S. Pat. No. 5,712,146 and which is a continuation-in-part ofU.S. Ser. No. 08/486,645 filed Jun. 7, 1995 which iscontinuation-in-part of U.S. Ser. No. 08/238,811 filed May 6, 1994,which issued Sep. 30, 1997 as U.S. Pat. No. 5,672,491. Priority isclaimed under 35 USC §120. Priority is also claimed under 35 USC 119(e)with respect to U.S. Provisional application No. 60/076,919 filed Mar.5, 1998. The disclosures of these applications are incorporated hereinby reference.

REFERENCE TO GOVERNMENT FUNDING

This work was supported in part by a grant from the National Institutesof Health, CA66736. The U.S. government has certain rights in thisinvention.

This work herein described was supported at least in part by the U.S.government under SBIR grant 1R43 CA 75792-01. The U.S. government hascertain rights to this invention.

TECHNICAL FIELD

The invention relates to the field of combinatorial libraries, to novelpolyketides and antibiotics and to methods to prepare them. Moreparticularly, it concerns construction of new polyketides and tolibraries of polyketides synthesized by polyketide synthases derivedfrom a naturally occurring PKS, as illustrated by the erythromycin genecluster.

BACKGROUND ART

Polyketides represent a large family of diverse compounds ultimatelysynthesized from 2-carbon units through a series of Claisen-typecondensations and subsequent modifications. Members of this groupinclude antibiotics such as tetracyclines, anticancer agents such asdaunomycin, and immunosuppressants such as FK506 and rapamycin.Polyketides occur in many types of organisms including fungi andmycelial bacteria, in particular, the actinomycetes.

A number of lactones of keto acids have been synthesized using standardorganic chemistry. These include a series of unsaturated ketolactonessynthesized by Vedejes et al., J. Am Chem Soc (1987) 109:5437-5446,shown as formulas 201, 202 and 203 in FIG. 11 herein. Additionalcompounds of formulas 204 and 205, also shown in FIG. 11 weresynthesized as reported by Vedejes et al. J Am Chem Soc (1989)111:8430-8438. In addition, compounds 206-208 (FIG. 11) were synthesizedby Borowitz, 1975, Mass spectra of 6-ketononanolides and relatedketolactones, J. Heterocyclic. Chem. 12(1): 101-106, compound 209 hasbeen synthesized by Ireland et al., J Org Chem (1980) 45:1868-1880.

The polyketides are synthesized in vivo by polyketide synthases (PKS).This group of enzymatically active proteins is considered in a differentcategory from the fatty acid synthases which also catalyze condensationof 2-carbon units to result in, for example, fatty acids andprostaglandins. Two major types of PKS are known which are vastlydifferent in their construction and mode of synthesis. These arecommonly referred to as Type I or “modular” and Type II, “aromatic.”

The PKS scaffold that is the subject of the present invention is amember of the group designated Type I or “modular” PKS. In this type, aset of separate active sites exists for each step of carbon chainassembly and modification, but the individual proteins contain amultiplicity of such separate active sites. There may be only onemultifunctional protein of this type, such as that required for thebiosynthesis of 6-methyl salicylic acid (Beck, J. et al., Eur J Biochem(1990) 192:487-498; Davis, R. et al., Abstracts of Genetics ofIndustrial Microorganism Meeting, Montreal, Abstract P288 (1994)). Morecommonly, and in bacterial-derived Type I PKS assemblies, there areseveral such multifunctional proteins assembled to result in the endproduct polyketide. (Cortes, J. et al., Nature (1990) 348:176; Donadio,S. et al., Science (1991) 252:675; MacNeil, D. J. et al., Gene (1992)115:119.)

A number of modular PKS genes have been cloned. U.S. Pat. No. 5,252,474describes cloning of genes encoding the synthase for avermectin; U.S.Pat. No. 5,098,837 describes the cloning of genes encoding the synthasefor spiramycin; European application 791,655 and European application791,656 describe the genes encoding the synthases for tylosin andplatenolide respectively.

The PKS for erythromycin, used as an illustrative system is a modularPKS. Erythromycin was originally isolated from S. erythraeus (sincereclassified as Saccharopolyspora erythraea) which was found in a soilsample from the Philippine archipelago. Cloning the genes was describedby Donadio, S. et al., Science (1991) 252:675. The particulars have beenreviewed by Perun, T. J. in Drug Action and Drug Resistance in Bacteria,Vol. 1, S. Mitsuhashi (ed.) University Park Press, Baltimore, 1977. Theantibiotic occurs in various glycosylated forms, designated A, B, C andD during various stages of fermentation. The entire erythromycinbiosynthetic gene cluster from S. erythraeus has been mapped andsequenced by Donadio et al. in Industrial Microorganisms: Basic andApplied Molecular Genetics (1993) R. H. Baltz, G. D. Hegeman, and P. L.Skatrud (eds.) (Amer Soc Microbiol) and the entire PKS is an assembly ofthree such multifunctional proteins usually designated DEBS-1, DEBS-2,and DEBS-3, encoded by three separate genes.

Expression of the genes encoding the PKS complex may not be sufficientto permit the production by the synthase enzymes of polyketides when thegenes are transformed into host cells that do not have the requiredauxiliary phosphopantetheinyl transferase enzymes whichposttranslationally modify the ACP domains of the PKS. Genes encodingsome of these transferases are described in WO97/13845. In addition,enzymes that mediate glycosylation of the polyketides synthesized aredescribed in WO97/23630. U.S. Ser. No. 08/989,332 filed Dec. 11, 1997now allowed describes the production of polyketides in hosts thatnormally do not produce them by supplying appropriatephosphopantetheinyl transferase expression systems. The contents of thisapplication are incorporated herein by reference.

There have been attempts to alter the polyketide synthase pathway ofmodular PKS clusters. For example, European application 238,323describes a process for enhancing production of polyketides byintroducing a rate-limiting synthase gene and U.S. Pat. No. 5,514,544describes use of an activator protein for the synthase in order toenhance production. U.S. Pat. Nos. 4,874,748 and 5,149,639 describeshuttle vectors that are useful in cloning modular PKS genes in general.Methods of introducing an altered gene into a microorganism chromosomeare described in WO93/13663. Modification of the loading module for theDEBS-1 protein of the erythromycin-producing polyketide synthase tosubstitute the loading module for the avermectin-producing polyketidesynthase in order to vary the starter unit was described by Marsden,Andrew F. A. et al. Science (1998) 279:199-202 and Oliynyk, M. et al.Chemistry and Biology (1996) 3:833-839. WO 98/01571, published Jan. 15,1998, describes manipulation of the erythromycin PKS and polyketidesresulting from such manipulation. In addition, WO 98/01546, alsopublished Jan. 15, 1998 describes a hybrid modular PKS gene for varyingthe nature of the starter and extender units to synthesize polyketides.

In addition, U.S. Pat. Nos. 5,063,155 and 5,168,052 describe preparationof antibiotics using modular PKS systems. A number of modular PKS havebeen cloned. See, e.g., U.S. Pat. No. 5,098,837, EP 791,655, EP 791,656and U.S. Pat. No. 5,252,474.

Type II PKS, in contrast to modular PKS, include several proteins, eachof which is simpler than those found in Type I polyketide synthases. Theactive sites in these enzymes are used iteratively so that the proteinsthemselves are generally monofunctional or bifunctional. For example,the aromatic PKS complexes derived from Streptomyces have so far beenfound to contain three proteins encoded in three open reading frames.One protein provides ketosynthase (KS) and acyltransferase (AT)activities, a second provides a chain length determining factor (CLDF)and a third is an acyl carrier protein (ACP).

The present invention is concerned with PKS systems derived from modularPKS gene clusters. The nature of these clusters and their manipulationare further described below.

DISCLOSURE OF THE INVENTION

The invention provides recombinant materials for the production ofcombinatorial libraries of polyketides wherein the polyketide members ofthe library are synthesized by various PKS systems derived fromnaturally occurring PKS systems by using these systems as scaffolds.Generally, many members of these libraries may themselves be novelcompounds, and the invention further includes novel polyketide membersof these libraries. The invention methods may thus be directed to thepreparation of an individual polyketide. The polyketide may or may notbe novel, but the method of preparation permits a more convenient methodof preparing it. The resulting polyketides may be further modified toconvert them to antibiotics, typically through glycosylation. Theinvention also includes methods to recover novel polyketides withdesired binding activities by screening the libraries of the invention.

Thus, in one aspect, the invention is directed to a method to prepare anucleic acid which contains a nucleotide sequence encoding a modifiedpolyketide synthase. The method comprises using a naturally occurringPKS encoding sequence as a scaffold and modifying the portions of thenucleotide sequence that encode enzymatic activities, either bymutagenesis, inactivation, or replacement. The thus modified nucleotidesequence encoding a PKS can then be used to modify a suitable host celland the cell thus modified employed to produce a polyketide differentfrom that produced by the PKS whose scaffolding has been used to supportmodifications of enzymatic activity. The invention is also directed topolyketides thus produced and the antibiotics to which they may then beconverted.

In another aspect, the invention is directed to a multiplicity of cellcolonies comprising a library of colonies wherein each colony of thelibrary contains an expression vector for the production of a differentmodular PKS, but derived from a naturally occurring PKS. In a preferredembodiment, the different PKS are derived from the erythromycin PKS. Inany case, the library of different modular PKS is obtained by modifyingone or more of the regions of a naturally occurring gene or gene clusterencoding an enzymatic activity so as to alter that activity, leavingintact the scaffold portions of the naturally occurring gene. Ifdesired, more than one scaffold source may be used, but basing thecluster of modules on a single scaffold is preferred. In another aspect,the invention is directed to a multiplicity of cell colonies comprisinga library of colonies wherein each colony of the library contains adifferent modular PKS derived from a naturally occurring PKS, preferablythe erythromycin PKS. The invention is also directed to methods toproduce libraries of PKS complexes and to produce libraries ofpolyketides by culturing these colonies, as well as to the libraries soproduced. In addition, the invention is directed to methods to screenthe resulting polyketide libraries and to novel polyketides containedtherein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A (SEQ ID NOS:1-3) is a diagram of the erythromycin PKS complexfrom S. erythraeus showing the function of each multifunctional protein,and also shows the structure of 6-deoxyerythronolide B (6dEB) and ofD-desosamine and L-cladinose.

FIG. 1B shows a diagram of the post-PKS biosynthesis of erythromycinsA-D.

FIG. 2 is a diagram of DEBS-1 from S. erythraeus showing the functionalregions separated by linker regions.

FIG. 3 shows a diagram of a vector containing the entire erythromycingene cluster.

FIG. 4 shows a method for the construction of the vector of FIG. 3.

FIG. 5 shows a diagram of the erythromycin gene cluster with locationsof restriction sites introduced for ease of manipulation.

FIGS. 6A-6H show the structures of polyketides produced by manipulatingthe erythromycin PKS gene cluster.

FIGS. 7A(SEQ ID NO:1), 7B(SEQ ID NO:4) and 7C(SEQ ID NOS:1-3) show theconstruction of derivative PKS gene clusters from the vector of FIG. 3.

FIGS 8A-8B show antibiotics obtained from selected polyketides shown inFIG. 6A-6F.

FIG. 9 shows a polyketide containing an unsaturated starter moiety andthe corresponding antibiotic.

FIG. 10 shows the preparation of a reagent used to glycosylatepolyketides to prepare the D-desosamine derivatives with antibioticactivity.

FIG. 11 shows the structures of known, previously produced, 12-membermacrolides.

FIGS. 12A and 12B show the structures of known and previously produced14-member macrolides.

DETAILED DESCRIPTION OF THE INVENTION

It may be helpful to review the nature of the erythromycin PKS complexand the gene cluster that encodes it as a model for modular PKS, ingeneral.

FIG. 1A is a diagrammatic representation of the gene cluster encodingthe synthase for the polyketide backbone of the antibiotic erythromycin.The erythromycin PKS protein assembly contains threehigh-molecular-weight proteins (>200 kD) designated DEBS-1, DEBS-2 andDEBS-3, each encoded by a separate gene (Caffrey et al., FEBS Lett(1992) 304:225). The diagram in FIG. 1A shows that each of the threeproteins contains two modules of the synthase—a module being that subsetof reactivities required to provide an additional 2-carbon unit to themolecule. As shown in FIG. 1A, modules 1 and 2 reside on DEBS-1; modules3 and 4 on DEBS-2 and modules 5 and 6 on DEBS-3. The minimal module istypified in module 3 which contains a ketosynthase (KS), anacyltransferase (AT) and an acyl carrier protein (ACP). These threefunctions are sufficient to activate an extender unit and attach it tothe remainder of the growing molecule. Additional activities that may beincluded in a module relate to reactions other than the Claisencondensation, and include a dehydratase activity (DH), an enoylreductaseactivity (ER) and a ketoreductase activity (KR). The first module alsocontains repeats of the AT and ACP activities because it catalyzes theinitial condensation, i.e. it begins with a “loading domain” representedby AT and ACP, which determine the nature of the starter unit. Althoughnot shown, module 3 has a KR region which has been inactivated bymutation. The “finishing” of the molecule is regulated by thethioesterase activity (TE) in module 6. This thioesterase appears tocatalyze cyclization of the macrolide ring thereby increasing the yieldof the polyketide product.

The product in this case is 6dEB, the structure and numbering system forthis molecule are shown in FIG. 1A. Conversion to the antibioticserythromycin A, B, C and D would require glycosylation generally byD-desosamine or L-mycarose, which is converted to cladinose inerythromycins A and B. FIG. 1B diagrams the post-PKS biosynthesis of theerythromycins through addition of glycosyl groups.

As shown, 6dEB is converted by the gene eryF to erythronolide B whichis, in turn, glycosylated by eryB to obtain 3-O-mycarosylerythronolide Bwhich contains L-mycarose at C-3. The enzyme eryC then converts thiscompound to erythromycin D by glycosylation with D-desosamine at C-5.Erythromycin D, therefore, differs from 6dEB through glycosylation andby the addition of a hydroxyl group at C-6. Erythromycin D can beconverted to erythromycin B in a reaction catalyzed by eryG bymethylating the L-mycarose residue at position 3. Erythromycin D isconverted to erythromycin C by the addition of a hydroxyl group at C-12.Erythromycin A is obtained from erythromycin C by methylation of themycarose residue catalyzed by eryG. The series of erythromycinantibiotics, then, differs by the level of hydroxylation of thepolyketide framework and by the methylation status of the glycosylresidues.

FIG. 2 shows a detailed view of the regions in the first two moduleswhich comprise the first open reading frame encoding DEBS-1. The regionsthat encode enzymatic activities are separated by linker or“scaffold”-encoding regions. These scaffold regions encode amino acidsequences that space the enzymatic activities at the appropriatedistances and in the correct order. Thus, these linker regionscollectively can be considered to encode a scaffold into which thevarious activities are placed in a particular order and spatialarrangement. This organization is similar in the remaining genes, aswell as in other naturally occurring modular PKS gene clusters.

The three DEBS-1, 2 and 3 proteins are encoded by the genetic segmentseryAI, eryAII, and eryAIII, respectively. These reading frames arelocated on the bacterial chromosome starting at about 10 kb distant fromthe erythromycin resistance gene (ermE or eryR).

The detailed description above referring to erythromycin is typical formodular PKS in general. Thus, rather than the illustrated erythromycin,the polyketide synthases making up the libraries of the invention can bederived from the synthases of other modular PKS, such as those whichresult in the production of rapamycin, avermectin, FK-506, FR-008,monensin, rifamycin, soraphen-A, spinocyn, squalestatin, or tylosin, andthe like.

Regardless of the naturally occurring PKS gene used as a scaffold, theinvention provides libraries or individual modified forms, ultimately ofpolyketides, by generating modifications in the erythromycin PKS orother naturally occurring PKS gene cluster so that the protein complexesproduced by the cluster have altered activities in one or more respects,and thus produce polyketides other than the natural product of the PKS.Novel polyketides may thus be prepared, or polyketides in generalprepared more readily, using this method. By providing a large number ofdifferent genes or gene clusters derived from a naturally occurring PKSgene cluster, each of which has been modified in a different way fromthe native cluster, an effectively combinatorial library of polyketidescan be produced as a result of the multiple variations in theseactivities. All of the PKS encoding sequences used in the presentinvention represent modular polyketide synthases “derived from” anaturally occurring PKS, illustrated by the erythromycin PKS. As will befurther described below, the metes and bounds of this derivation can bedescribed on both the protein level and the encoding nucleotide sequencelevel.

By a modular PKS “derived from” the erythromycin or other naturallyoccurring PKS is meant a modular polyketide synthase (or itscorresponding encoding gene(s)) that retains the scaffolding of all ofthe utilized portion of the naturally occurring gene. (Not all modulesneed be included in the constructs.) On the constant scaffold, at leastone enzymatic activity is mutated, deleted or replaced, so as to alterthe activity. Alteration results when these activities are deleted orare replaced by a different version of the activity, or simply mutatedin such a way that a polyketide other than the natural product resultsfrom these collective activities. This occurs because there has been aresulting alteration of the starter unit and/or extender unit, and/orstereochemistry, and/or chain length or cyclization and/or reductive ordehydration cycle outcome at a corresponding position in the productpolyketide. Where a deleted activity is replaced, the origin of thereplacement activity may come from a corresponding activity in adifferent naturally occurring polyketide synthase or from a differentregion of the same PKS. In the case of erythromycin, for example, any orall of the DEBS-1, DEBS-2 and DEBS-3 proteins may be included in thederivative or portions of any of these may be included; but thescaffolding of an erythromycin PKS protein is retained in whateverderivative is considered. Similar comments pertain to the correspondingeryAI, eryAII, and eryAIII genes.

The derivative may contain preferably at least a thioesterase activityfrom the erythromycin or other naturally occurring PKS gene cluster.

In summary, a polyketide synthase “derived from” a naturally occurringPKS contains the scaffolding encoded by all or the portion employed ofthe naturally occurring synthase gene, contains at least two modulesthat are functional, preferably three modules, and more preferably fouror more modules and contains mutations, deletions, or replacements ofone or more of the activities of these functional modules so that thenature of the resulting polyketide is altered. This definition appliesboth at the protein and genetic levels. Particular preferred embodimentsinclude those wherein a KS, AT, KR, DR or ER has been deleted orreplaced by a version of the activity from a different PKS or fromanother location within the same PKS. Also preferred are derivativeswhere at least one noncondensation cycle enzymatic activity (KR, DR orER) has been deleted or wherein any of these activities has been mutatedso as to change the ultimate polyketide synthesized.

Thus, there are five degrees of freedom for constructing a polyketidesynthase in terms of the polyketide that will be produced. First, thepolyketide chain length will be determined by the number of modules inthe PKS. Second, the nature of the carbon skeleton of the PKS will bedetermined by the specificities of the acyl transferases which determinethe nature of the extender units at each position—e.g., malonyl,methylmalonyl, or ethylmalonyl, etc. Third, the loading domainspecificity will also have an effect on the resulting carbon skeleton ofthe polyketide. Thus, the loading domain may use a different starterunit, such as acetyl, propionyl, and the like. Fourth, the oxidationstate at various positions of the polyketide will be determined by thedehydratase and reductase portions of the modules. This will determinethe presence and location of ketone, alcohol, double bonds or singlebonds in the polyketide. Finally, the stereochemistry of the resultingpolyketide is a function of three aspects of the synthase. The firstaspect is related to the AT/KS specificity associated with substitutedmalonyls as extender units, which affects stereochemistry only when thereductive cycle is missing or when it contains only a ketoreductasesince the dehydratase would abolish chirality. Second, the specificityof the ketoreductase will determine the chirality of any β-OH. Finally,the enoyl reductase specificity for substituted malonyls as extenderunits will influence the result when there is a complete KR/DH/ERavailable.

In the working examples below, the foregoing variables for varyingloading domain specificity which controls the starter unit, a usefulapproach is to modify the KS activity in module 1 which results in theability to incorporate alternative starter units as well as module 1extended units. This approach was illustrated in PCT applicationUS96/11317, published Jan. 23, 1997 as WO 97/02358 wherein the KS-Iactivity was inactivated through mutation. Polyketide synthesis is theninitiated by feeding chemically synthesized analogs of module 1 diketideproducts. Working examples of this aspect are also presentedhereinbelow.

Thus, the modular PKS systems, and in particular, the erythromycin PKSsystem, permit a wide range of polyketides to be synthesized. Ascompared to the aromatic PKS systems, a wider range of starter unitsincluding aliphatic monomers (acetyl, propionyl, butyryl, isovaleryl,etc.), aromatics (aminohydroxybenzoyl), alicyclics (cyclohexanoyl), andheterocyclics (thiazolyl) are found in various macrocyclic polyketides.Recent studies have shown that modular PKSs have relaxed specificity fortheir starter units (Kao el al. Science (1994), supra). Modular PKSsalso exhibit considerable variety with regard to the choice of extenderunits in each condensation cycle. The degree of β-ketoreductionfollowing a condensation reaction has also been shown to be altered bygenetic manipulation (Donadio et al. Science (1991), supra; Donadio, S.et al. Proc Natl Acad Sci USA (1993) 90:7119-7123). Likewise, the sizeof the polyketide product can be varied by designing mutants with theappropriate number of modules (Kao, C. M. et al. J Am Chem Soc (1994)116:11612-11613). Lastly, these enzymes are particularly well-known forgenerating an impressive range of asymmetric centers in their productsin a highly controlled manner. The polyketides and antibiotics producedby the methods of the present invention are typically singlestereoisomeric forms. Although the compounds of the invention can occuras mixtures of stereoisomers, it is more practical to generateindividual stereoisomers using this system. Thus, the combinatorialpotential within modular PKS pathways based on any naturally occurringmodular, such as the erythromycin, PKS scaffold is virtually unlimited.

In general, the polyketide products of the PKS must be further modified,typically by glycosylation, in order to exhibit antibiotic activity.Methods for glycosylating the polyketides are generally known in theart; the glycosylation may be effected intracellularly by providing theappropriate glycosylation enzymes or may be effected in vitro usingchemical synthetic means.

The antibiotic modular polyketides may contain any of a number ofdifferent sugars, although D-desosamine, or a close analog thereof, ismost common. Erythromycin, picromycin, narbomycin and methymycin containdesosamine. Erythromycin also contains L-cladinose (3-O-methylmycarose). Tylosin contains mycaminose (4-hydroxy desosamine), mycaroseand 6-deoxy-D-allose. 2-acetyl-1-bromodesosamine has been used as adonor to glycosylate polyketides by Masamune et al. J Am Chem Soc (1975)97:3512, 3513. Other, apparently more stable, donors include glycosylfluorides, thioglycosides, and trichloroacetimidates; Woodward, R. B. etal. J Am Chem Soc (1981) 103:3215; Martin, S. F. et al. Am Chem Soc(1997) 119:3193; Toshima, K. et al. J Am Chem Soc (1995) 117:3717;Matsumoto, T. et al. Tetrahedron Lett (1988) 29:3575. Glycosylation canalso be effected using the macrolides as starting materials and usingmutants of S. erythraea that are unable to synthesize the macrolides tomake the conversion. A method is illustrated in the Exampleshereinbelow.

Methods to Construct Multiple Modular PKS Derived from a NaturallyOccurring PKS

The derivatives of the a naturally occurring PKS can be prepared bymanipulation of the relevant genes. A large number of modular PKS geneclusters have been mapped and/or sequenced, including erythromycin,soraphen A, rifamycin, and rapamycin, which have been completely mappedand sequenced, and FK506 and oleandomycin which have been partiallysequenced, and candicidin, avermectin, and nemadectin which have beenmapped and partially sequenced. Additional modular PKS gene clusters areexpected to be available as time progresses. These genes can bemanipulated using standard techniques to delete or inactivate activityencoding regions, insert regions of genes encoding correspondingactivities from the same or different PKS system, or otherwise mutatedusing standard procedures for obtaining genetic alterations. Of course,portions of, or all of, the desired derivative coding sequences can besynthesized using standard solid phase synthesis methods such as thosedescribed by Jay, E., et al., J Biol Chem (1984) 259:6311-6317 and whichare available commercially from, for example, Applied Biosystems, Inc.

In order to obtain nucleotide sequences encoding a variety ofderivatives of the naturally occurring PKS, and thus a variety ofpolyketides for construction of a library, a desired number ofconstructs can be obtained by “mixing and matching” enzymaticactivity-encoding portions, and mutations can be introduced into thenative host PKS gene cluster or portions thereof.

Mutations can be made to the native sequences using conventionaltechniques. The substrates for mutation can be an entire cluster ofgenes or only one or two of them; the substrate for mutation may also beportions of one or more of these genes. Techniques for mutation includepreparing synthetic oligonucleotides including the mutations andinserting the mutated sequence into the gene encoding a PKS subunitusing restriction endonuclease digestion. (See, e.g., Kunkel, T. A. ProcNatl Acad Sci USA (1985) 82:448, Geisselsoder et al. Bio Techniques(1987) 5:786.) Alternatively, the mutations can be effected using amismatched primer (generally 10-20 nucleotides in length) whichhybridizes to the native nucleotide sequence (generally cDNAcorresponding to the RNA sequence), at a temperature below the meltingtemperature of the mismatched duplex. The primer can be made specific bykeeping primer length and base composition within relatively narrowlimits and by keeping the mutant base centrally located. Zoller andSmith, Methods Enzymol (1983) 100:468. Primer extension is effectedusing DNA polymerase, the product cloned and clones containing themutated DNA, derived by segregation of the primer extended strand,selected. Selection can be accomplished using the mutant primer as ahybridization probe. The technique is also applicable for generatingmultiple point mutations. See, e.g., Dalbie-McFarland et al. Proc NatlAcad Sci USA (1982) 79:6409. PCR mutagenesis will also find use foreffecting the desired mutations.

Random mutagenesis of selected portions of the nucleotide sequencesencoding enzymatic activities can be accomplished by several differenttechniques known in the art, e.g., by inserting an oligonucleotidelinker randomly into a plasmid, by irradiation with X-rays orultraviolet light, by incorporating incorrect nucleotides during invitro DNA synthesis, by error-prone PCR mutagenesis, by preparingsynthetic mutants or by damaging plasmid DNA in vitro with chemicals.Chemical mutagens include, for example, sodium bisulfite, nitrous acid,nitrosoguanidine, hydroxylamine, agents which damage or remove basesthereby preventing normal base-pairing such as hydrazine or formic acid,analogues of nucleotide precursors such as 5-bromouracil, 2-aminopurine,or acridine intercalating agents such as proflavine, acriflavine,quinacrine, and the like. Generally, plasmid DNA or DNA fragments aretreated with chemicals, transformed into E. coli and propagated as apool or library of mutant plasmids.

In addition to providing mutated forms of regions encoding enzymaticactivity, regions encoding corresponding activities from different PKSsynthases or from different locations in the same PKS synthase can berecovered, for example, using PCR techniques with appropriate primers.By “corresponding” activity encoding regions is meant those regionsencoding the same general type of activity—e.g., a ketoreductaseactivity in one location of a gene cluster would “correspond” to aketoreductase-encoding activity in another location in the gene clusteror in a different gene cluster, similarly, a complete reductase cyclecould be considered corresponding—e.g., KR/DH/ER would correspond to KRalone.

If replacement of a particular target region in a host polyketidesynthase is to be made, this replacement can be conducted in vitro usingsuitable restriction enzymes or can be effected in vivo usingrecombinant techniques involving homologous sequences framing thereplacement gene in a donor plasmid and a receptor region in a recipientplasmid. Such systems, advantageously involving plasmids of differingtemperature sensitivities are described, for example. in PCT PublicationWO 96/40968.

The vectors used to perform the various operations to replace theenzymatic activity in the host PKS genes or to support mutations inthese regions of the host PKS genes may be chosen to contain controlsequences operably linked to the resulting coding sequences in a mannerthat expression of the coding sequences may be effected in a appropriatehost. However, simple cloning vectors may be used as well.

If the cloning vectors employed to obtain PKS genes encoding derived PKSlack control sequences for expression operably linked to the encodingnucleotide sequences, the nucleotide sequences are inserted intoappropriate expression vectors. This need not be done individually, buta pool of isolated encoding nucleotide sequences can be inserted intohost vectors, the resulting vectors transformed or transfected into hostcells and the resulting cells plated out into individual colonies.

Suitable control sequences include those which function in eucaryoticand procaryotic host cells. Preferred hosts include fungal systems suchas yeast and procaryotic hosts, but single cell cultures of, forexample, mammalian cells could also be used. There is no particularadvantage, however, in using such systems. Particularly preferred areyeast and procaryotic hosts which use control sequences compatible withStreptomyces spp. Suitable controls sequences for single cell culturesof various types of organisms are well known in the art. Control systemsfor expression in yeast, including controls which effect secretion arewidely available and routinely used. Control elements include promoters,optionally containing operator sequences, and other elements dependingon the nature of the host, such as ribosome binding sites. Particularlyuseful promoters for procaryotic hosts include those from PKS geneclusters which result in the production of polyketides as secondarymetabolites, including those from aromatic (Type II) PKS gene clusters.Examples are act promoters, tcm promoters, spiramycin promoters, and thelike. However, other bacterial promoters, such as those derived fromgenes that encode sugar metabolizing enzymes, such as galactose, lactose(lac) and maltose, are also useful. Additional examples includepromoters derived from genes that encode biosynthetic enzymes forcompounds such as tryptophan (trp), and the β-lactamase (bla),bacteriophage lambda PL, and T5 prompters. In addition, syntheticpromoters, such as the tac promoter (U.S. Pat. No. 4,551,433), can beused.

Other regulatory sequences may also be desirable which allow forregulation of expression of the PKS replacement sequences relative tothe growth of the host cell. Regulatory sequences are known to those ofskill in the art, and examples include those which cause the expressionof a gene to be turned on or off in response to a chemical or physicalstimulus, including the presence of a regulatory compound. Other typesof regulatory elements may also be present in the vector, for example,enhancer sequences.

Selectable markers can also be included in the recombinant expressionvectors. A variety of markers are known which are useful in selectingfor transformed cell lines and generally comprise a gene whoseexpression confers a selectable phenotype on transformed cells when thecells are grown in an appropriate selective medium. Such markersinclude, for example, genes which confer antibiotic resistance orsensitivity to the plasmid. Alternatively, several polyketides arenaturally colored and this characteristic provides a built-in marker forscreening cells successfully transformed by the present constructs.

The various PKS nucleotide sequences, or a cocktail of such sequences,can be cloned into one or more recombinant vectors as individualcassettes, with separate control elements, or under the control of,e.g., a single promoter. The PKS subunits or cocktail components caninclude flanking restriction sites to allow for the easy deletion andinsertion of other PKS subunits or cocktail components so that hybridPKSs can be generated. The design of such unique restriction sites isknown to those of skill in the art and can be accomplished using thetechniques described above, such as site-directed mutagenesis and PCR.

As described above, particularly useful control sequences are thosewhich themselves, or using suitable regulatory systems, activateexpression during transition from growth to stationary phase in thevegetative mycelium. The system contained in the illustrated plasmidpCK7, i.e., the actI/actIII promoter pair and the actII-ORF4, anactivator gene, is particularly preferred. Particularly preferred hostsare those which lack their own means for producing polyketides so that acleaner result is obtained. Illustrative host cells of this type includethe modified S. coelicolor CH999 culture described in PCT publication WO96/40968 and similar strains of S. lividans.

The expression vectors containing nucleotide sequences encoding avariety of PKS systems for the production of different polyketides arethen transformed into the appropriate host cells to construct thelibrary. In one straightforward approach, a mixture of such vectors istransformed into the selected host cells and the resulting cells platedinto individual colonies and selected for successful transformants. Eachindividual colony will then represent a colony with the ability toproduce a particular PKS synthase and ultimately a particularpolyketide. Typically, there will be duplications in some of thecolonies; the subset of the transformed colonies that contains adifferent PKS in each member colony can be considered the library.Alternatively, the expression vectors can be used individually totransform hosts, which transformed hosts are then assembled into alibrary. A variety of strategies might be devised to obtain amultiplicity of colonies each containing a PKS gene cluster derived fromthe naturally occurring host gene cluster so that each colony in thelibrary produces a different PKS and ultimately a different polyketide.The number of different polyketides that are produced by the library istypically at least four, more typically at least ten, and preferably atleast 20, more preferably at least 50, reflecting similar numbers ofdifferent altered PKS gene clusters and PKS gene products. The number ofmembers in the library is arbitrarily chosen; however, the degrees offreedom outlined above with respect to the variation of starter,extender units, stereochemistry, oxidation state, and chain length allowquite large libraries.

Methods for introducing the recombinant vectors of the present inventioninto suitable hosts are known to those of skill in the art and typicallyinclude the use of CaCl₂ or other agents, such as divalent cations,lipofection, DMSO, protoplast transformation and electroporation.

As disclosed in copending application Ser. No. 08/989,332 filed Dec. 11,1997 now U.S. Pat. No. 6,035,883, incorporated herein by reference, awide variety of hosts can be used, even though some hosts natively donot contain the appropriate post-translational mechanisms to activatethe acyl carrier proteins of the synthases. These hosts can be modifiedwith the appropriate recombinant enzymes to effect these modifications.

The polyketide producing colonies can be identified and isolated usingknown techniques and the produced polyketides further characterized. Thepolyketides produced by these colonies can be used collectively in apanel to represent a library or may be assessed individually foractivity.

The libraries can thus be considered at four levels: (1) a multiplicityof colonies each with a different PKS encoding sequence encoding adifferent PKS cluster but all derived from a naturally occurring PKScluster; (2) colonies which contain the proteins that are members of thePKS produced by the coding sequences; (3) the polyketides produced; and(4) antibiotics derived from the polyketides. Of course, combinationlibraries can also be constructed wherein members of a library derived,for example, from the erythromycin PKS can be considered as a part ofthe same library as those derived from, for example, the rapamycin PKScluster.

Colonies in the library are induced to produce the relevant synthasesand thus to produce the relevant polyketides to obtain a library ofcandidate polyketides. The polyketides secreted into the media can bescreened for binding to desired targets, such as receptors, signalingproteins, and the like. The supernatants per se can be used forscreening, or partial or complete purification of the polyketides canfirst be effected. Typically, such screening methods involve detectingthe binding of each member of the library to receptor or other targetligand. Binding can be detected either directly or through a competitionassay. Means to screen such libraries for binding are well known in theart.

Alternatively, individual polyketide members of the library can betested against a desired target. In this event, screens wherein thebiological response of the target is measured can more readily beincluded.

Indeed, a large number of novel polyketides have been prepared accordingto the method of the invention as illustrated in the examples below.These novel polyketides are useful intermediates in formation ofcompounds with antibiotic activity through glycosylation reactions asdescribed above. As indicated above, the individual polyketides arereacted with suitable sugar derivatives to obtain compounds withantibiotic activity. Antibiotic activity can be verified using typicalscreening assays such as those set forth in Lehrer, R. et al. J ImmunolMeth (1991) 137:167-173.

New polyketides which are the subject of the invention are thosedescribed below. New antibiotics which are the subject of the inventioninclude the glycosylated forms of these polyketides.

In one embodiment, the polyketides of the invention include thecompounds of structure (1) and the glycosylated forms thereof. Thecompounds include the polyketide structure:

including the isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹ and R² is independently H or alkyl (1-4C) wherein any alkylat R¹ may optionally be substituted;

X¹ is H₂, HOH or ═O;

with the provisos that:

at least one of R¹ and R² must be alkyl (1-4C); and

the compound is other than compounds 1, 2, 3, 5 and 6 of FIG. 6A.

Particularly preferred embodiments of formula (1) include compound 4shown in FIG. 6A.

In another embodiment, the polyketides of the invention include thecompounds of formula (2) and the glycosylated forms thereof. Thesecompounds include the polyketide structure:

including the isolated stereoisomeric forms thereof,

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-5C;

each of R¹, R² and R³ is independently H or alkyl (1-4C) wherein anyalkyl at R¹ may optionally be substituted;

each of X¹ and X² is independently H₂, HOH or ═O;

with the proviso that:

at least two of R¹, R² and R³ are alkyl (1-4C).

In another embodiment, the polyketides of the invention include thecompounds of structure (3) and the glycosylated forms thereof. Thecompounds include the polyketide structure:

including the isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-5C,

each of R¹, R² and R³ is independently H or alkyl (1-4C) wherein anyalkyl at R¹ may optionally be substituted,

each of X¹ and X² is independently H₂, HOH or ═O;

with the provisos that:

at least one of R¹ and R² must be alkyl (1-4C); and

the compound is other than compound 8 of FIG. 6A.

The antibiotic forms of the polyketide of formula (3) are thecorresponding glycosylated forms.

Still other embodiments are those of the following formula, includingthe glycosylated forms thereof. These are derived from the compound offormula (4) which has the structure:

including the isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹, R² and R³ is independently H or alkyl (1-4C) wherein anyalkyl at R¹ may optionally be substituted;

each of X* and X² is independently H₂, HOH or ═O;

with the provisos that:

at least one of R² and R³ is alkyl (1-4C); and

the compound is other than compound 9 of FIG. 6A.

Still other embodiments are the result of the condensation of fivemodules of the polyketide synthase system. The polyketide forms of thesecompounds are of the formula:

including the glycosylated and isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹, R², R³, R⁴ and R⁵ is independently H or alkyl (1-4C) whereinany alkyl at R¹ may optionally be substituted;

each of X¹, X², X³ and X⁴ is independently H₂, HOH or ═O; or

X¹ or X² or X³ or X⁴ is H and the compound of formula (5) contains aπ-bond at positions 8-9 or 6-7 or 4-5 or 2-3;

with the provisos that:

at least two of R¹-R⁵ are alkyl (1-4C); and

the compound is other than compound 13 or 14 of FIG. 6A or compound 205,210-213 of FIG. 11.

Preferred forms of compounds of formula (5) are those wherein at leastthree, more preferably at least four, of R¹-R⁵ are alkyl (1-4C),preferably methyl or ethyl.

Also preferred are compounds wherein X¹ is —OH and/or X2is ═O, and/or X³is H.

The glycosylated forms of these compounds are also useful antibiotics.

Resulting from the condensation effected by six modules are thecompounds which comprise the formula:

including the glycosylated and isolated stereoisomeric forms thereof,

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹-R⁶ is independently H or alkyl (1-4C) wherein any alkyl at R¹may optionally be substituted;

each of X¹-X⁵ is independently H₂, HOH or ═O; or

each of X¹-X⁵ is independently H and the compound of formula (5)contains a π-bond in the ring adjacent to the position of said X at 2-3,4-5, 6-7, 8-9 and/or 10-11;

with the proviso that:

at least two of R¹-R⁶ are alkyl (1-4C); and

the compound is other than compound 17, 24 or 28 of FIG. 6B, compound301-311 of FIG. 12(A) or compounds 312-322of FIG. 12(B).

Preferred compounds comprising formula 6 are those wherein at leastthree of R¹-R⁵ are alkyl (1-4C), preferably methyl or ethyl, morepreferably wherein at least four of R¹-R⁵ are alkyl (1-4C), preferablymethyl or ethyl.

Also preferred are those wherein X² is H₂, ═O or H . . . and/or X3 is H,and/or X¹ is OH and/or X⁴ is OH and/or X⁵ is OH.

Particularly preferred are compounds of formulas 18-23, 25-27, 29-75 and101 and 113 of FIGS. 6B-6F. Also preferred are compounds with variableR* when R¹-R⁵ are methyl, X² is ═O, and X¹, X⁴ and X⁵ are OH examples ofwhich are depicted in formulas 96-100 and 104-107 of FIGS. 6G and 6H.The glycosylated forms of the foreoging are also preferred.

Other polyketides which result from the condensation catalyzed by sixmodules of a modular PKS include those of the formula:

including the glycosylated and isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹-R⁵ is independently H or alkyl (1-4C) wherein any alkyl at R¹may optionally be substituted;

R⁶ is alkyl (1-5C);

each of X¹ and X³ and X⁶ is independently H₂, HOH or ═O;

with the proviso that:

at least two of R¹-R⁴ are alkyl (1-4C).

These and their corresponding glycosylated forms are also included inthe invention.

Still others include those of the formula:

including the isolated stereoisomeric forms thereof;

wherein R* is a straight chain, branched or cyclic, saturated orunsaturated substituted or unsubstituted hydrocarbyl of 1-15C;

each of R¹-R⁵ is independently H or alkyl (1-4C) wherein any alkyl at R¹may optionally be substituted;

R⁶ is alkyl (1-5C);

X² is OH or H;

each X¹, X³, X⁴ and X⁵ is independently H₂, HOH or ═O; or X³ or X⁴ is Hand the compound of formula (8) has a π-bond between positions 7-8 or9-10, with the proviso that:

if X² is H, at least one of X³ and X⁴ is HOH or ═O.

These and their corresponding glycosylated forms are also included inthe invention.

As above, the glycosylated forms are useful antibiotics.

As set forth above, R* in the compounds of the invention may besubstituted as well as unsubstituted. Suitable substituents include halo(F, Cl, Br, I), N₃, OH, O-alkyl (1-6C); S-alkyl (1-6C), CN, O-acyl(1-7C), O-aryl (6-10C), O-alkyl-aryl (7-14C), NH₂, NH-alkyl (1-6C) andN-(alkyl)₂.

Suitable substituents on R¹ are selected from the same group as thosefor R* In addition, the substituents on R¹ and R* may form a ring systemsuch as an epoxide ring, or a larger heterocyclic ring including O, or Nor S. Preferred substituents for R* and R¹ are halo, OH and NH₂.Unsubstituted forms are also preferred.

Particularly useful as antibiotics within the scope of the invention arecompounds of formulas 82-93 as set forth in FIG. 8 herein.

Still another embodiment of the compounds of the invention is set forthas compound 94 in FIG. 9. Its glycosylated form, shown as compound 95,is useful as an antibiotic.

Examples

The following examples are intended to illustrate, but not to limit theinvention.

MATERIALS AND METHODS GENERAL TECHNIQUES

Bacterial Strains, Plasmids, and Culture Conditions

S. coelicolor CH999 described in WO 95/08548, published Mar. 30, 1995was used as an expression host. DNA manipulations were performed inEscherichia coli MC1061. Plasmids were passaged through E. coli ET 12567(dam dcm hsdS Cm^(r)) (MacNeil, D. J. J Bacteriol (1988) 170:5607) togenerate unmethylated DNA prior to transformation of S. coelicolor. E.coli strains were grown under standard conditions. S. coelicolor strainswere grown on P2YE agar plates (Hopwood, D. A. et al. Geneticmanipulation of Streptomyces. A laboratory manual. The John InnesFoundation: Norwich, 1985). pRM5, also described in WO 95/08548,includes a colEI replicon, an appropriately truncated SCP2* Streptomycesreplicon, two act-promoters to allow for bidirectional cloning, the geneencoding the actII-ORF4 activator which induces transcription from actpromoters during the transition from growth phase to stationary phase,and appropriate marker genes. Engineered restriction sites facilitatethe combinatorial construction of PKS gene clusters starting fromcassettes encoding individual domains of naturally occurring PKSs.

When pRM5 is used for expression of PKS, (i) all relevant biosyntheticgenes are plasmid-borne and therefore amenable to facile manipulationand mutagenesis in E. coli, (ii) the entire library of PKS gene clusterscan be expressed in the same bacterial host which is genetically andphysiologically well-characterized and presumably contains most, if notall, ancillary activities required for in vivo production ofpolyketides, (iii) polyketides are produced in a secondarymetabolite-like manner, thereby alleviating the toxic effects ofsynthesizing potentially bioactive compounds in vivo, and (iv) moleculesthus produced undergo fewer side reactions than if the same pathwayswere expressed in wild-type organisms or blocked mutants.

Manipulation of DNA and Organisms

Polymerase chain reaction (PCR) was performed using Taq polymerase(Perkin Elmer Cetus) under conditions recommended by the enzymemanufacturer. Standard in vitro techniques were used for DNAmanipulations (Sambrook, et al. Molecular Cloning: A Laboratory Manual(Current Edition)). E. coli was transformed with a Bio-Rad E. ColiPulsing apparatus using protocols provided by Bio-Rad. S. coelicolor wastransformed by standard procedures (Hopwood, D. A. et al. Geneticmanipulation of Streptomyces. A laboratory manual. The John InnesFoundation: Norwich, 1985) and transformants were selected using 2 mL ofa 500 μg/ml thiostrepton overlay.

PREPARATION A Construction of the Complete Erythromycin PKS Gene ClusterRecovery of the Erythromycin PKS Genes

Although various portions of the erythromycin PKS gene cluster can bemanipulated separately at any stage of the process of preparinglibraries, it may be desirable to have a convenient source of the entiregene cluster in one place. Thus, the entire erythromycin PKS genecluster can be recovered on a single plasmid if desired. This isillustrated below utilizing derivatives of the plasmid pMAK705 (Hamiltonet al. J Bacteriol (1989) 171:4617) to permit in vivo recombinationbetween a temperature-sensitive donor plasmid, which is capable ofreplication at a first, permissive temperature and incapable ofreplication at a second, non-permissive temperature, and recipientplasmid. The eryA genes thus cloned gave pCK7, a derivative of pRM5(McDaniel et al Science (1993) 262:1546). A control plasmid, pCK7f, wasconstructed to carry a frameshift mutation in eryAI. pCK7 and pCK7fpossess a ColEI replicon for genetic manipulation in E. coli as well asa truncated SCP2* (low copy number) Streptomyces replicon.

These plasmids also contain the divergent actI/actIII promoter pair andactII-ORF4, an activator gene, which is required for transcription fromthese promoters and activates expression during the transition fromgrowth to stationary phase in the vegetative mycelium. High-levelexpression of PKS genes occurs at the onset of the stationary phase ofmycelial growth. The recombinant strains therefore produce the encodedpolyketides as secondary metabolites.

In more detail, pCK7 (FIG. 3), a shuttle plasmid containing the completeeryA genes, which were originally cloned from pS1 (Tuan et al. Gene(1990) 90:21), was constructed as follows. The modular DEBS PKS geneswere transferred incrementally from a temperature-sensitive “donor”plasmid, i.e., a plasmid capable of replication at a first, permissivetemperature and incapable of replication at a second, non-permissivetemperature, to a “recipient” shuttle vector via a double recombinationevent, as depicted in FIG. 4. A 25.6 kb SphI fragment from pS1 wasinserted into the SphI site of pMAK705 (Hamilton et al. J Bacteriol(1989) 171:4617) to give pCK6 (Cm^(R)), a donor plasmid containingeryAII, eryAIII, and the 3′ end of eryAI. Replication of thistemperature-sensitive pSC101 derivative occurs at 30° C. but is arrestedat 44° C. The recipient plasmid, pCK5 (Ap^(R), Tc^(R)), includes a 12.2kb eryA fragment from the eryAI start codon (Caffrey et al. FEBS Lett(1992) 304:225) to the XcmI site near the beginning of eryAII, a 1.4 kbEcoRI-BsmI pBR322 fragment encoding the tetracycline resistance gene(Tc), and a 4.0 kb NotI-EcoRI fragment from the end of eryAII. PacI,NdeI, and ribosome binding sites were engineered at the eryAI startcodon in pCK5. pCK5 is a derivative of pRM5 (described above). The 5′and 3′ regions of homology are 4.1 kb and 4.0 kb, respectively. MC1061E. coli was transformed with pCK5 and pCK6 and subjected tocarbenicillin and chloramphenicol selection at 30° C. Colonies harboringboth plasmids (Ap^(R), Cm^(R)) were then restreaked at 44° C. oncarbenicillin and chloramphenicol plates. Only cointegrates formed by asingle recombination event between the two plasmids were viable.Surviving colonies were propagated at 30° C. under carbenicillinselection, forcing the resolution of the cointegrates via a secondrecombination event. To enrich for pCK7 recombinants, colonies wererestreaked again on carbenicillin plates at 44° C. Approximately 20% ofthe resulting colonies displayed the desired phenotype (Ap^(R), Tc^(S),Cm^(S)). The final pCK7 candidates were thoroughly checked viarestriction mapping. A control plasmid, pCK7f, which contains aframeshift error in eryAI, was constructed in a similar manner. pCK7 andpCK7f were transformed into E. coli ET12567 (MacNeil J Bacteriol (1988)170:5607) to generate unmethylated plasmid DNA and subsequently movedinto Streptomyces coelicolor CH999.

Upon growth of CH999/pCK7 on R2YE medium, the organism produced abundantquantities of two polyketides. The addition of propionate (300 mg/L) tothe growth medium resulted in approximately a two-fold increase in yieldof polyketide product. Proton and ¹³C NMR spectroscopy, in conjunctionwith propionic-1-¹³C acid feeding experiments, confirmed the majorproduct as 6dEB (>40 mg/L) (FIG. 1A). The minor product was identifiedas 8,8a-deoxyoleandolide (>10 mg/L) (FIG. 1A), which apparentlyoriginates from an acetate starter unit instead of propionate in the6dEB biosynthetic pathway. ¹³C₂ sodium acetate feeding experimentsconfirmed the incorporation of acetate into the minor product. Threehigh molecular weight proteins (>200 kDa), presumably DEBS1, DEBS2, andDEBS3 (Caffrey et al. FEBS Lett (1992) 304:225), were also observed incrude extracts of CH999/pCK7 via SDS-polyacrylamide gel electrophoresis.No polyketide products were observed from CH999/pCK7f. The inventorshereby acknowledge support provided by the American Cancer Society(IRG-32-34).

Example 1 Preparation of Scaffolds for Replacing DEBS AT and KR Domains

For each of the six modules of DEBS, a subclone was made containingendonuclease restriction sites engineered at selected boundaries of theacyltransferase (AT) and reduction (KR or DH/ER/KR) domains. Therestriction sites were introduced into the subclones by PCR mutagenesis.A BamHI site was used for the 5′ boundary of AT domains, a PstI site wasintroduced between the AT and reductive domains, and XbaI was used atthe 3′ end of the reductive domain (see FIG. 5). This resulted in thefollowing engineered sequence (SEQ ID NO: 5-22) indicates engineeredrestriction site):

Module 1 (pKOS011-16) 5′ AT boundary GCGCAGCAGggatccGTCTTCGTC AT/KRboundary CGCGTCTGGctgcagCCGAAGCCG 3′ KR boundaryCCGGCCGAAtctagaGTGGGCGCG Module 2 (pKOS001-11) 5′ AT boundaryTCCGACGGTggatccGTGTTCGTC AT/KR boundary CGGTTCTGGctgcagCCGGACCGC 3′ KRboundary ACGGAGAGCtctagaGACCGGCTG Module 3 (pKOS024-2) 5′ AT boundaryGACGGGCGCggatccGTCTTCCTG AT/KR boundary CGCTACTGGctgcagCCCGCCGCA 3′ KRboundary ACCGGCGAGtctagaCAACGGCTC Module 4 (pKOS024-3) 5′ AT boundaryGCGCCGCGCggatccGTCCTGGTC AT(DH/ER/KR) boundary CGCTTCTGGctgcagCCGCACCGG3′ DH/ER/KR boundary GGGCCGAACtctagaGACCGGCTC Module 5 (pKOS006-182) 5′AT boundary ACTCGCCGCggatccGCGATGGTG AT/KR boundaryCGGTACTGGctgcagATCCCCACC 3′ KR boundary GAGGAGGGCtctagaCTCGCCCAG Module6 (pKOS015-52) 5′ AT boundary TCCGCCGGCggatccGTTTTCGTC AT/KR boundaryCGGTACTGGctgcagCCGGAGGTG 3′ KR boundary GTGGGGGCCtctagaGCGGTGCAG

Example 2 Preparation of Cassettes from the Rapamycin PKS

A cosmid library of genomic DNA from Streptomyces hygroscopicus ATCC29253 was used to prepare DNA cassettes prepared from the rapamycin PKSgene cluster to be used as replacements into the enzymatic activityregions of the erythromycin gene cluster. Cassettes were prepared by PCRamplification from appropriate cosmids or subclones using the primerpairs listed in Table 1, and were designed to introduce suitablerestriction sites at the ends of the cassettes. The rapAT2 cassette isflanked by BglII and PstI sites, and the rapAT14 cassette is flanked byBamHI and PstI sites. The reductive cycle cassettes are flanked by PstIand XbaI sites. Large DH/ER/KR cassettes were amplified in two pieces,then joined at an engineered XhoI site in order to minimize errorsintroduced during PCR amplification of long DNA sequences. The rapKR4cassette was made by cloning a 1.3 kb NheI/XbaI fragment from therapDH/KR4 cassette above into the XbaI site in pUC19. There is a PstIsite that is in-frame and upstream of XbaI in pUC19 that generates thefollowing junction at the 5′-end of the cassette:

5′-ctgcagGTCGACTCTAGCCTGGT (SEQ ID NO: 23) . . .

TABLE 1 Primer pairs used for PCR amplification of rapamycin PKScassettes. All primers are listed from 5′ to 3′. Engineered restrictionsites are lower case. Module Primer Sequence (SEQ ID NOS:24-35) rapAT2forward: TTTagatctTGTTCGTCTTCCCGGGT Reverse:TTTctgcagCCAGTACCGCTGGTGCTGGAAGGCGTA rapAT14 Forward:TTTggatccGCCTTCCTGTTCGACGGGCAAGGC Reverse:TTTctgcagCCAGTAGGACTGGTGCTGGAACGG rapKR2 Forward:TTTctgcagGAGGGCACGGACCGGGCGACTGCGGGT Reverse:TTTtctagaACCGGCGGCAGCGGCCCGCCGAGCAAT rapDH/KR4 Forward:TTctgcagAGCGTGGACCGGGCGGCT Reverse: TTTtctagaGTCACCGGTAGAGGCGGCCCTrapDH/ER/KR1 Forward: TTTctgcagGGCGTGGACCGGGCGGCTGCC (left half)Reverse: TTTctcgagCACCACGCCCGCAGCCTCACC rapDH/ER/KR1 Forward:TTTctcgagGTCGGTCCGGAGGTCCAGGAT (right half) Reverse:TTTtctagaATCACCGGTAGAAGCAGCCCG

Example 3 Replacement of DEBS Modules By Rapamycin PKS Cassettes

The following are typical procedures. The products are indicated bytheir numbers in FIG. 6 as well as listed in Table 2, below, where “a”represents the embodiment where R is methyl; “b” represents theembodiment where R is hydrogen.

a) Replacement of DEBS DH/ER/KR4. A portion of the erythromycin gene ofmodule 4 (eryDH/ER/KR4) was replaced either with the correspondingrapamycin activities of the first rapamycin module (rapDH/ER/KR1) or ofmodule 4 of rapamycin (rapDH/KR4). The replacement utilized thetechnique of Kao et al. Science (1994) 265:509-512. A donor plasmid wasprepared by first amplifying 1 kbp regions flanking the DH/ER/KR4 ofDEBS to contain a PstI site at the 3′ end of the left flank and an XbaIsite at the 5′ end of the right flank. The fragments were ligated into atemperature-sensitive donor plasmid, in a manner analogous to that setforth for KR6 in paragraph b) of this example, and the rapamycincassettes prepared as described in Example 2 were inserted into thePstI/XbaI sites. The recipient plasmid was pCK7 described in PreparationA. The in vivo recombination technique resulted in the expressionplasmid pKOS011-19 (eryDH/ER/KR4→rapDH/ER/KR1) and pKOS011-21(eryDF/ER/KR4→rapDH/KR4). The junctions at which the PstI and XbaI siteswere introduced into DEBS in both vectors are as follows (SEQ ID NOS:36-37)

GAGCCCCAGCGGTACTGGCTGCAG rap cassette TCTAGAGCGGTGCAGGCGGCCCCG

The resulting expression vectors were transformed into S. coelicolorCH999 and successful transformants grown as described above. Thetransformant containing the rapDH/ER/KR1 cassette produced thepolyketide shown FIG. 6 as compound 23 and listed in Table 2 as 24a,b,the transformant containing the plasmid with rapDH/KR4 cassette producedthe polyketide shown in FIG. 6 as compound 24 and listed in Table 2 as24a,b. As shown, these polyketides differ from 6-deoxyerythronolide B byvirtue of a 6,7 alkene in the case of 24a and by the C6-methylstereochemistry in the case of 23a.

b) Replacement of DEBS KR6. In a manner analogous to that set forth inparagraph a), plasmid pKOS011-25, wherein eryKR6 was replaced byrapDH/KR4, was prepared by substituting regions flanking the KR6 domainof DEBS in construction of the donor plasmid.

Approximately 1 kb regions flanking the eryKR6 domain were PCR amplifiedwith the following primers (SEQ ID NOS: 38-41).

left forward 5′-TTTGGATCCGTTTTCGTCTTCCCAGGTCAG flank reverse5′-TTTCTGCAGCCAGTACCGCTGGGGCTCGAA right forward5′-TTTTCTAGAGCGGTGCAGGCGGCCCCGGCG flank reverse5′-AAAATGCATCTATGAATTCCCTCCGCCCA

These fragments were then cloned into a pMAK705 derivative in which themultiple cloning site region was modified to accommodate the restrictionsites of the fragments (i.e., BamHI/PstI for the left flank andXbaI/NsiI for the right flank). Cassettes were then inserted into thePstI/XbaI sites of the above plasmid to generate donor plasmids for thein vivo recombination protocol. The resulting PstI and XbaI junctionsengineered into DEBS are as follows (SEQ ID NOS: 42-43)

GAACACCAGCGCTTCTGGCTGCAG rap cassette TCTAGAGACCGGCTCGCCGGTCGG

Regions flanking the KR6 domain of DEBS were used to construct the donorplasmids.

Transformants of S. coelicolor CH999 resulted in the production of thepolyketide shown in FIG. 6 as compound 74 and listed in Table 2 as74a,b.

c) Replacement of DEBS KR2. The eryKR2 enzymatic activity was replacedin a series of vectors using in vitro insertion into the PstI/XbaI sitesof pKAO263. pKAO263 is a derivative of pCK13 described in Kao, C. M. JAm Chem Soc (1996) 118:9184-9185. It was prepared by introducing thePstI and XbaI restriction sites positioned identically to those in theanalogous 2-module DEBS system described by Bedford, D. et al. Chem anBiol (1996) 3:827-831. Three expression plasmids were prepared:pKOS009-7 (eryKR2→rapDH/KR4); pKAO392 (eryKR2→rapKR2); and pKAO410(eryKR2→rapDH/ER/KR1). These plasmids, when transformed into S.coelicolor CH999, resulted in the production of polyketides with thestructures 12a,b; 3a,b; and 10a, 11a,b listed in Table 2 and shown inFIG. 6, respectively. An additional vector, pKAO400 (eryKR2→rapKR4)produced the same results as pKAO392.

d) Replacement of DEBS AT2. The DEBS AT activity from module 2 wasexcised after inserting restriction sites BamHI and PstI flanking the ATmodule 2 domain into pCK12 (Kao et al. J Am Chem Soc (1995)112:9105-9106). After digestion with BamHI/PstI, the BglII/PstI fragmentcontaining rapAT2 was inserted. The resulting engineered DEBS/rapAT2junction is as follows (BamHI/BglII ligation-GGATCT; PstI-CTGCAG) (SEQID NOS: 44-45)

AGTGCCTCCGACGGTGGATCT rapAT2 CTGCAGCCGGACCGCACCACCCCT

S. coelicolor CH999 transformed with the resulting plasmid, pKOS008-51,produced the polyketides 6a,b shown in FIG. 6 as structure 6.

Example 4 Excision of DEBS Reductive Cycle Domains

The following is a typical procedure. The products are indicated bytheir numbers in FIG. 6, and listed in Table 2 where “a” represents theembodiment where R is methyl; “b” represents the embodiment where R ishydrogen.

A duplex oligonucleotide linker (ΔRdx) was designed to allow completeexcision of reductive cycle domains. Two synthetic oligonucleotides (SEQID NOS: 46-47):

5′-GCCGGACCGCACCACCCCTCGTGACGGAGAACCGGAGACGGAGAGCT-3′3′-ACGTCGGCCTGGCGTGGTGGGGAGCACTGCCTCTTGGCCTCTGCCTCTCGAGATC-5′       PstI                                             XbaI

were designed to generate PstI- and XbaI-compatible ends uponhybridization. This duplex linker was ligated into the PstI- andXbaI-sites of the recombination donor plasmid containing the appropriateleft- and right-flanking regions of the reductive domain to be excised.The in vivo recombination technique of Example 3, paragraph a) was thenused. The donor plasmid contained the duplex linker ΔRdx having a PstIand XbaI compatible end ligated into the PstI and XbaI sites of theplasmid modified to contain the left and right flanking regions of thereductive domain to be excised. The donor plasmids were recombined withrecipient plasmid pCK7 to generate pKOS011-13 (eryKR6→ΔRdx) and withrecipient plasmid pCK13 to obtain pKOS005-4 (eryKR2→ΔRdx). Whentransformed into S. coelicolor CH999, plasmid pKOS011-13 produced thepolyketide listed in Table 2 as 30a,b, 31a,b, 77a,b, and 78a,b and shownin FIG. 6 as structures 30, 31, 77, and 78; plasmid pKOS005-4 producedthe polyketide listed in Table 2 as 2a,b and shown in FIG. 6 asstructure 2.

Example 5 Manipulation of Macrolide Ring Size by Directed Mutagenesis ofDEBS

The following are typical procedures. The products are indicated bytheir numbers in FIG. 6, and listed in Table 2 where “a” represents theembodiment where R is methyl; “b” represents the embodiment where R ishydrogen.

Using the expression system of Kao, C. M. et al. Science (1994)265:509-512, the expression of DEBS1 alone (1+2), in the absence ofDEBS2 and DEBS3 (in plasmid pCK9), resulted in the production of(2R,3S,4S,5R)-2,4-dimethyl-3,5-dihydroxy-n-heptanoic acid L-lactone(“the heptanoic acid L-lactone” (see FIGS. 6 and 7)) (1-3 mg/L), theexpected triketide product of the first two modules (Kao, C. M. et al. JAm Chem Soc (1994) 116:11612-11613). Thus, a thioesterase is notessential for release of a triketide from the enzyme complex.

Two additional deletion mutant PKS were constructed. The first containedDEBS1 fused to the TE, and the second PKS included the first five DEBSmodules fused to the TE. Plasmids pCK12 and pCK15 respectively containedthe genes encoding the bimodular (“1+2+TE”) and pentamodular(“1+2+3+4+5+TE”) PKSs.

The 1+2+TE PKS in pCK12 contained a fusion of the carboxy-terminal endof the acyl carrier protein of module 2 (ACP-2) to the carboxy-terminalend of the acyl carrier protein of module 6 (ACP-6). Thus ACP-2 isessentially intact and is followed by the amino acid sequence naturallyfound between ACP-6 and the TE. Plasmid pCK12 contained eryA DNAoriginating from pS1 (Tuan, J. S. et al. Gene (1990) 90:21). pCK12 isidentical to pCK7 (Kao et al. Science (1994), supra) except for adeletion between the carboxy-terminal ends of ACP-2 and ACP-6. Thefusion occurs between residues L3455 of DEBS1 and Q2891 of DEBS3. AnSpeI site is present between these two residues so that the DNA sequenceat the fusion is CTCACTAGTCAG (SEQ ID NO:48).

The 1+2+3+4+5+TE PKS in pCK15 contained a fusion 76 amino acidsdownstream of the β-ketoreductase of module 5 (KR-5) and five aminoacids upstream of ACP-6. Thus, the fusion occurs towards thecarboxy-terminal end of the non-conserved region between KR-5 and ACP-5,and the recombinant module 5 was essentially a hybrid between the wildtype modules 5 and 6. Plasmid pCK15 contained eryA DNA originating frompS1 (Tuan et al. Gene (1990), supra). pCK15 is a derivative of pCK7 (Kaoet al. Science (1994), supra) and was constructed using the in vivorecombination strategy described earlier (Kao et al. Science (1994),supra). pCK15 is identical to pCK7 with the exception of a deletionbetween KR-5 and ACP-6, which occurs between residues G1372 and A2802 ofDEBS3, and the insertion of a blunted a SalI fragment containing akanamycin resistance gene (Oka A. et al. J Mol Biol (1981) 147:217) intothe blunted HindIII site of pCK7. An arginine residue is present betweenG1372 and A2802 so that the DNA sequence at the fusion is GGCCGCGCC.

Plasmids pCK12 and pCK15 were introduced into S. coelicolor CH999 andpolyketide products were purified from the transformed strains accordingto methods previously described (Kao et al. Science (1994), supra). Theproducts obtained from various transformants: CH999/pCK12 andCH999/pCK15 as well as CH999/pCK9 described above, are shown in FIG. 7.

CH999/pCK12 produced the heptanoic acid L-lactone (1a) (20 mg/L) asdetermined by ¹H and ¹³C NMR spectroscopy. This triketide product isidentical to that produced by CH999/pCK9, which expresses the unmodifiedDEBS1 protein alone described above. However, CH999/pCK12 producedcompound 1a (compound 1, where R is methyl, in FIG. 6) in significantlygreater quantities than did CH999/pCK9 (>10 mg/L vs.˜mg/L), indicatingthe ability of the TE to catalyze thiolysis of a triketide chainattached to the ACP domain of module 2. CH999/pCK12 also producedsignificant quantities of compound 1b, a novel analog of compound 1a,(10 mg/L), that resulted from the incorporation of an acetate start unitinstead of propionate. This is reminiscent of the ability of CH999/pCK7,which expresses the intact PKS, to produce 8,8a-deoxyoleandolide (seeFIG. 1A) in addition to 6dEB described above.

Since compound 1b was not detected in CH999/pCK9, its facile isolationfrom CH999/pCK12 provides additional evidence for the increased turnoverrate of DEBS1 due to the presence of the TE. In other words, the TE caneffectively recognize an intermediate bound to a “foreign” module thatis four acyl units shorter than its natural substrate, 6dEB. However,since the triketide products can probably cyclize spontaneously intocompound 1a and 1b under typical fermentation conditions (pH 7), it isnot possible to discriminate between a biosynthetic model involvingenzyme-catalyzed lactonization and one involving enzyme-catalyzedhydrolysis followed by spontaneous lactonization. Thus, the ability ofthe 1+2+TE PKS to recognize the C-5 hydroxyl of a triketide as anincoming nucleophile is unclear.

CH999/pCK15, produced abundant quantities of(8R,9S)-8,9-dihydro-8-methyl-9-hydroxy-10-deoxymethonolide (compound 13in FIG. 6) (10 mg/L), demonstrating that the pentamodular PKS is active.Compound 13 was characterized using ¹H and ¹³C NMR spectroscopy ofnatural abundance and ¹³C-enriched material, homonuclear correlationspectroscopy (COSY), heteronuclear correlation spectroscopy (HETCOR),mass spectrometry, and molecular modeling. Compound 13 is an analog of10-deoxymethonolide (compound 14, Lambalot, R. H. et al. J Antibiotics(1992) 45:1981-1982), the aglycone of the macrolide antibioticmethymycin. The production of compound 13 by a pentamodular enzymedemonstrates that active site domains in modules 5 and 6 in DEBS can bejoined without loss of activity. Thus, it appears that individualmodules as well as active sites are independent entities which do notdepend on association with neighboring modules to be functional. The12-membered lactone ring, formed by esterification of the terminalcarboxyl with the C-11 hydroxyl of the hexaketide product, indicated theability of the 1+2+3+4+5+TE PKS, and possibly the TE itself, to catalyzelactonization of a polyketide chain one acyl unit shorter,than thenatural product of DEBS, 6dEB. Indeed, the formation of compound 13 maymimic the biosynthesis of the closely related 12-membered hexaketidemacrolide, methymycin, which frequently occurs with the homologous14-membered heptaketide macrolides, picromycin and/or narbomycin (Cane,D. E. et al. J Am Chem Soc (1993) 115:522-566). The erythromycin PKSscaffold can thus be used to generate a wide range of macrolactones withshorter as well as longer chain lengths.

The construction of the 1+2+3+4+5+TE PKS resulted in the biosynthesis ofa previously uncharacterized 12-membered macrolactone that closelyresembles, but is distinct from, the aglycone of a biologically activemacrolide. The apparent structural and functional independence of activesite domains and modules as well as relaxed lactonization specificitysuggest the existence of many degrees of freedom for manipulating theseenzymes to produce new modular PKSs.

Example 6 Production and Analysis of Polyketide Products

The expression vectors created by domain substitution in DEBS, asdescribed in Examples 1-5, were transformed into either Streptomycescoelicolor CH999 or S. lividans K4-114 using standard techniques (D. A.Hopwood et al. (1985) “Genetic Manipulation of Streptomyces: ALaboratory Manual,” (The John Innes Foundation, Norwich)). Both hoststrains have complete deletions of the native actinorhodin polyketidesynthase gene cluster and so produce no native polyketide products.Transformants were grown on 150 mm R2YE agar plates for 2 days at 30°C., at which time the agar slab was lifted from the dish and placed in anew dish which contained a layer of 4 mm glass beads, 50 mL of liquidR2YE medium supplemented with 5 mM sodium propionate, and ca. 1 g ofXAD-16 resin beads. This was kept at 30° C. for an additional 7 days.

The XAD-16 resin was collected by vacuum filtration, washed with water,then extracted twice with 10 mL portions of ethanol. The extracts werecombined and evaporated to a slurry, which was extracted with ethylacetate. The ethyl acetate was washed once with sat. NaHCO₃ andevaporated to yield the crude product. Samples were dissolved in ethanoland analyzed by LC/MS. The HPLC used a 4.6×150 mm C18 reversed-phasecolumn with a gradient from 80:19:1 H₂O/CH₃CN/CH₃CO₂H to 99:1CH₃CN/CH₃CO₂H. Mass spectra were recorded using a Perkin-Elmer/SciexAPI100LC spectrometer fitted with an APCI ion source. Each geneticconstruct typically resulted in formation of products in pairs,indicated in Table 2 by the letters “a” (R=CH3) and “b” (R=H), arisingfrom priming of the PKS by and propionyl-CoA and acetyl-CoA,respectively.

Additional Examples

Using the foregoing techniques, the DEBS constructs shown in Table 2were prepared. The products obtained when the constructs weretransformed into S. coelicolor CH999 are indicated by their numbers inFIG. 6 and in Table 2, where “a” represents the embodiment where R ismethyl; “b” represents the embodiment where R is hydrogen. Some of theexpression vectors were prepared by in vitro ligation; multiple domainsubstitutions were created by subsequent in vitro ligations into thesingly-substituted expression plasmids. Others were obtained by in vivorecombination.

TABLE 2 Products Plasmid Modules Domain Substitution (see FIG. 6) InVitro Ligation KOS011-28 2 eryAT1 → rapAT2 4-nor-TKL (5a, b) KOS008-51 2eryAT2 → rapAT2 2-nor-TKL (6a, b) KOS014-62 2 eryKR2 → rapDH/ER/KR13-deoxy-TKL (4a, b) KAO410 3 eryKR2 → rapDH/ER/KR1 KAO410 (10a, b)3-deoxy-hemiketal (11a, b) KAO392 3 eryKR2 → rapKR2 3-epi-TKL (3a, b)KOS009-7 3 eryKR2 → rapDH/KR4 KOS009-7 (12a, b) KOS015-30 6 eryAT3 →rapAT2 8-nor-6dEB (18a, b) KOS016-47 6 eryAT5 → rapAT2 4-nor-6dEB (19a,b) KOS026-18b 6 eryKR5 → rapDH/ER/KR1 5-deoxy-6dEB (26a, b) KOS016-32 6eryKR5 → rapDH/KR4 4,5-anhydro-6dEB (27a, b) KOS016-28 6 eryKR5 → ΔRdx5-oxo-6dEB (28a, b) KOS015-63 6 eryAT6 → rapAT2 2-nor-6dEB (20a, b)KOS015-83 6 eryAT2 → rapAT2 + 10-nor-10,11-anhydro-6dEB (32a, b) eryKR2→ rapDH/KR4 KOS015-84 6 eryAT2 → rapAT2 + 10-nor-11-deoxy-6dEB (33a, b)eryKR2 → rapDH/ER/KR1 KOS016-100 6 eryAT5 → rapAT2 + 4-nor-5-oxo-6dEB(38a, b) eryKR5 → Δrdx KOS015-106 6 eryAT6 → rapAT2 + 2-nor-3-epi-6dEB(42a, b) eryKR6 → rapKR2 KOS015-109 6 eryAT6 → rapAT2 + 2-nor-3-oxo-6dEB(31a, b) eryKR6 → Δrdx KOS011-90 6 eryAT2 → rapAT2 +4,5-dehydro-10-nor-6dEB (34a, b) eryKR5 → rapDH/KR4 KOS011-84 6 eryAT2 →rapAT2 + 5-oxo-10-nor-6dEB (35a, b) eryKR5 → Δrdx KOS011-82 6 eryKR2 →rapDH/KR4 + 4-nor-10,11-dehydro-6dEB (39a, b) eryAT5 → rapAT2 KOS011-856 eryKR2 → rapDH/KR4 + 5-oxo-10,11-dehydro-6dEB (57a, b) eryKRS → ΔrdxKOS011-87 6 eryKR2 → rapDH/KR4 + 4-nor-5-oxo-10,11-anhydro-6dEB (65a, b)eryAT5 → rapAT2 + eryKR5 → Δrdx KOS011-83 6 eryKR2 → rapDH/ER/KR1 +4-nor-11-deoxy-6dEB (40a, b) eryAT5 → rapAT2 KOS011-91 6 eryKR2 →rapDH/ER/KR1 + 4,5-anhydro-11-deoxy-6dEB (55a, b) eryKR5 → rapDH/KR4KOS011-86 6 eryKR2 → rapDH/ER/KR1 + 5-oxo-11-deoxy-6dEB (56a, b) eryKR5→ Δrdx KOS011-88 6 eryKR2 → rapDH/ER/KR1 + 4-nor-5-oxo-11-deoxy-6dEB(69a, b) eryAT5 → rapAT2 eryKR5 → Δrdx KOS015-40 6 eryAT2 → rapAT2 +2,3-anhydro-10-nor-6dEB (76a, b) eryKR6 → rapDH/KR4 KOS015-41 6 eryAT2 →rapAT2 + 3-oxo-1O-nor-6dEB (36a, b) eryKR6 → Δrdx 10-nor-spiroketal(79a, b) KOS015-44 6 eryKR2 → rapDH/ER/KR1 + 2-nor-11-deoxy-6dEB (45a,b) eryAT6 → rapAT2 KOS015-45 6 eryKR2 → rapDH/ER/KR1 +2,3-anhydro-11-deoxy-6dEB (75a, b) eryKR6 → RapDH/KR4 KOS015-46 6 eryKR2→ rapDH/ER/KR1 + 3-oxo-11-deoxy-6dEB (53a, b) eryKR6 → Δrdx KOS015-42 6eryKR2 → rapDH/KR4 + 2-nor-10,11-anhydro-6dBE (46a, b) eryAT6 → rapAT2KOS015-43 6 eryKR2 → rapDH/KR4 + 3-oxo-10,11-anhydro-6dEB (54a, b)eryKR8 → Δrdx KOS015-88 6 eryKR2 → rapDH/KR4 + 3-epi-10,11-anhydro-6dEB(48a, b) eryKR6 → rapKR2 KOS015-89 6 eryKR2 → rapDH/ER/KR1 +3-epi-11-deoxy-6dEB (49a, b) eryKR6 → rapKR2 KOS015-87 6 eryAT2 →rapAT2 + 3-oxo-10-nor-6dEB (36a, b) eryKR6 → rapKR2 KOS015-117 6 eryAT2→ rapAT14 + 2,10-bisnor-6dEB (37a, b) eryAT6 → rapAT2 KOS015-120 6eryAT2 → rapAT14 + 2,10-bisnor-3-oxo-6dEB (58a, b) eryAT6 → rapAT2 +2,10-bisnor-spiroketal (80a, b) eryKR6 → Δrdx KOS015-121 6 eryKR2 →rapDH/KR4 + 2-nor-3-epi-10,11-dehydro-6dEB eryAT6 → rapAT2 + (62a, b)eryKR6 → rapKR2 KOS015-122 6 eryKR2 → rapDH/KR4 +2-nor-3-oxo-10,11-dehydro-6dEB eryAT6 → rapAT2 + (63a, b) eryKR6 → ΔrdxKOS015-123 6 eryKR2 → rapDH/ER/KR1 + 2-nor-3-epi-11-deoxy-6dEB (66a, b)eryAT6 → rapAT2 + eryKR6 → rapKR2 KOS015-125 6 eryKR2 → rapDH/ER/KR1 +2-nor-3-oxo-11-deoxy-6dEB (67a, b) eryAT6 → rapAT2 + eryKR6 → ΔrdxKOS015-127 6 eryAT2 → rapAT2 + 3-epi-10-nor-10,11-dehydro-6dEB eryKR2 →rapDH/KR4 + (64a, b) eryKR6 → rapKR2 KOS015-150 6 eryAT2 → rapAT2 +2,10-bisnor-10,11-dehydro-6dEB eryKR2 → rapDH/KR4 + (59a, b) eryAT6 →rapAT2 KOS015-158 6 eryAT2 → rapAT2 + 3-oxo-10-nor-11-deoxy-6dEB (68a,b) eryKR2 → rapDH/ER/KR1 + eryKR6 → Δrdx KOS015-159 6 eryAT2 → rapAT2 +2,10-bisnor-11-deoxy-6dEB (60a, b) eryKR2 → rapDH/ER/KR1 + eryAT6 →rapAT2 KOS016-133K 6 eryKR5 → rapDH/KR4 + 3-oxo-4,5-dehydro-6dEB (51a,b) eryKR6 → Δrdx 3,5-dioxo-6dEB (52a, b) KOS016-150B 6 eryKR5 → Δrdx +3-epi-5-oxo-6dEB (50a, b) eryKR6 → rapKR4 KOS016-183F 6 eryAT5 →rapAT2 + 2,4-bisnor-6dEB (41a, b) eryAT6 → rapAT2 KOS016-183G 6 eryAT5 →rapAT2 + 2,4-bisnor-3-epi-6dEB (61a, b) eryAT6 → rapAT2 + eryKR6 →rapKR2 KOS016-152E 6 eryKR5 → rapDH/KR4 + 2-nor-4,5-dehydro-6dEB (43a,b) eryAT6 → rapAT2 KOS016-152F 6 eryKR5 → rapDH/KR4 +2-nor-3-epi-4,5-dehydro-6dEB eryAT6 → rapAT2 + (70a, b) eryKR6 → rapKR2KOS016-152G 6 eryKR5 → rapDH/KR4 + 2-nor-3-oxo-4,5-dehydro-6dEB eryAT6 →rapAT2 + (71a, b) eryKR6 → Δrdx hemiketal (81a, b) KOS016-152K 6 eryKR5→ Δrdx + 2-nor-5-oxo-6dEB (44a, b) eryAT6 → rapAT2 KOS016-152I 6 eryKR5→ Δrdx + 2-nor-3-epi-5-oxo-6dEB (72a, b) eryAT6 → rapAT2 + eryKR6 →rapKR2 KOS015-34 6 eryAT3 → rapAT2 + 2,8-bisnor-6dEB (47a, b) eryAT6 →rapAT2 KOS015-162 6 eryKR2 → rapDH/ER/KR1 + 2-nor-5-oxo-11-deoxy-6dEB(73a, b) eryKRS → Δrdx + eryAT6 → rapAT2 In Vivo Ligation KOS005-4 3 KR2→ ΔRdx 3-keto-TKL (2a, b) KOS011-62 6 AT2 → rapAT2 10-nor-6dEB (17a, b)KOS011-66 6 KR2 → rapDH/ER/KR1 11-deoxy-6dEB (21a, b) KOS011-64 6 KR2 →rapDH/KR4 10,11-dehydro-6dEB (22a, b) KOS011-19 6 DH/ER/KR4 → 6-epi-6dEB(23a, b) rapDH/ER/KR1 KOS011-21 6 DH/ER/KR4 → 6,8-dehydro-6dEB (24a, b)rapDH/KR4 KOS011-22 6 DH/ER/KR4 → ΔRdx 7-oxo-6dEB (25a, b) KOS011-74 6KR6 → rapKR2 3-epi-6dEB (29a, b) KOS011-25 6 KR6 → rapDH/KR42,3-anhydro-6dEB (74a, b) KOS011-13 6 KR6 → ΔRdx 3-oxo-6dEB (30a, b)2-nor-3-oxo-6dEB (31 a, b) spiroketal (77a, b) 2-nor-spiroketal (78a, b)

Example 7 Preparation of 14,15-dehydro-6-deoxyerythronolide B (Compound94 of FIG. 9)

A 3 day culture of S. coelicolor CH999/pJRJ2 grown on 3 100-mm R2YE agarplates was overlayed with a solution of 10 mgof(2S,3R)-3-hydroxy-2-methyl-4-pentenoic acid N-acetylcysteaminethioester dissolved in 2 mL of 9:1 water/DMSO and allowed to dry. Theculture was incubated at 30° C. for an additional 4 days. The agar waschopped and extracted twice with an equal volume of ethyl acetate. Theextracts were combined and evaporated. Purification by silica gelchromatography (1:1 ethyl acetate/hexanes) yielded 0.75 mg of14,15-dehydro-6-deoxyerythronolide B, compound 94 in FIG. 9, APCI-MSgives [M+H]+=385.

Analogous compounds with variations in R* and/or R¹ as represented bycompounds 96-107 and compound 113 of FIGS. 6G and 6H are prepared in asimilar manner as described in the previous paragraph but substitutingthe appropriate diketide as the N-acetylcysteamine thioester. Thesecompounds are prepared in this manner and their structures verified.

The preparation of the appropriate derivatized diketides is described inExample 17.

Example 8 Synthesis of1-(2-mercaptopyrimidinyl)-2-O-methoxycarbonyl-(D)-desosamine

For the glycosylation reactions in the following examples, the titlecompound was used as a reagent. The conversions of paragraph (A) and (B)of this Example are shown in FIG. 10.

(A) Preparation of 1,2-di-O-methoxycarbonyl-(D)-desosamine

To 1.00 g of (D)-desosamine (4.74 mmol) in 50 mL CH₂Cl₂ was added 3.06 gof diisopropylethylamine. The mixture was stirred at ambient temperaturefor 10 min, then cooled to 4° C. Methyl chloroformate (1.34 g) was addeddropwise at 4° C. The reaction mixture was allowed to warm to ambienttemperature and stirred overnight. The solvent was evaporated todryness, ethyl acetate (150 mL) was added to extract the product, andthe remaining solid was filtered. The ethyl acetate was removed undervacuum and the crude product was purified on a silica gel column (ethylacetatemethanol:triethylamine 84:5:1 v/v/v) to give 1.29 g of product(88% yield).

(B) Preparation of1-(2-mercaptopyrimidinyl)-2-O-methoxycarbonyl-(D)-desosamine

A mixture of 1,2-di-O-methoxycarbonyl-(D)-desosamine (1.00 g, 3.436mmol) and 0.7697 g of 2-mercaptopyrimdine (6.872 mmol) in a 25 mL 2-neckflash is dried under vacuum for 45 minutes. Dichloroethane (10 mL),toluene (5 mL), and DMF (5 mL) were added and stirred at ambienttemperature followed by addition of 7 mL of SnCl₄ (1M in CH₂Cl₂). Thereaction mixture was kept at 80° C. overnight. The reaction wasterminated by addition of 1N NaOH until the mixture turned basic. Thesolution was extracted with 300 mL of ethyl acetate and the organiclayer was washed with saturated aqueous NaHCO₃ (3×150 mL), dried overNa₂SO₄, filtered, and evaporated. The product was purified on a silicagel column (1:1 ethyl acetate:hexanes to ethyl acetate with 1%triethylamine) to obtain 0.25 g of1-(2-mercaptopyrimidinyl)-2-O-methoxycarbonyl-(D)-desosamine and 0.5 gof recovered 1,2-di-O-methoxycarbonyl-(D)-desosamine.

Example 9 Preparation of5-O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)]-6-deoxyerythronolide Band 5-O-(1-β-(D)-desosaminyl)-deoxyerythronolide B (Compounds 86 and 87in FIG. 8)

(A) A mixture of 6-deoxyerythronolide B (6-dEB) (15 mg, 39 umol) and1-(2-mercaptopyrimidinyl)-2-O-methoxycarbonyl-(D)-desosamine (65 mg, 200umol) was dried under vacuum, then placed under a nitrogen atmosphere.To this was added CH₂Cl₂ (1 mL), toluene (0.5 mL), and powdered 4Amolecular sieves (50 mg), and the mixture was stirred for 10 minutes atambient temperature. Silver trifluoromethanesulfonate (64 mg, 250 umol)was added and the reaction was stirred until LC/MS analysis indicatedcompletion (18-20 hours). The mixture was filtered through anhydrousNa₂SO₄ and evaporated to yield crude product. The residue was dissolvedin several drops of acetonitrile and loaded on a C-18 solid phaseextraction cartridge (Whatman). Unreacted desosamine was removed bywashing with 20% CH₃CN/H₂O and glycosylation products and the remainingmacrolide aglycone were recovered by eluting with 100% CH₃CN. Finalseparation was carried out by HPLC using a semiprep C-18 column (10mm×150 mm) (CH₃CN/H₂O, 20% isocratic over 5 min, then 20% to 80% over 30min). HPLC fractions were checked by LC/MS and fractions containing thesame product were combined. The solvent was removed under vacuum,yielding 8.4 mg of5-O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)]-6-deoxy-erythronolide B(compound 86 in FIG. 8) (36% yield). APCI-MS gives [M+H]+=602.

(B) 5-O-[1-(2-O-methoxycarbonyl-(D)-desosaminyl)]-6-deoxyerythronolide B(1-6 mg) from paragraph (A) was dissolved in 1 mL methanol, 0.2 mL H2O,and 0.2 mL triethylamine and kept at 70° C. for 3 hours. Removal of thesolvent under vacuum gave crude product. This was dissolved in a fewdrops of CH₃CN and applied to a Whatman C18 solid phase extractioncartridge. The column was washed with 25 mL of 20% CH₃CN in water, thenthe product was eluted with 100% CH₃CN. Evaporation of the solvent gave5-O-(1-β-(D)-desosaminyl)-6-deoxyerythronolide B (compound 87 in FIG. 8)in quantitative yield. APCl-MS gives [M+H+=544.

Example 10 Preparation of5-O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)]-8,8a-deoxyoleandolideand 5-O-(1-β-(D)-desosaminyl)]-8,8a-deoxyoleandolide (Compounds 88 and89 in FIG. 8)

(A) Treatment of 8,8a-deoxyoleandolide (12 mg) as described in Example9(A) yielded5-O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)]-8,8a-deoxyoleandolide(60% yield) (compound 88 in FIG. 8). APCI-MS gives [M+H]+=508.

(B) Treatment of5-O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)]-8,8a-deoxyoleandolide ofparagraph (A) as described in Example 9(B) gave5-O-(1-β-(D)-desosaminyl)-8,8a-deoxyoleandolide (compound 89 in FIG. 8)in quantitative yield. APCI-MS gives [M+H]+=530.

Example 11 Preparation of5-O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)]-3,6-dideoxy-3-oxoerythronolideB (Compound 90 in FIG. 8) and5,11-bis-(O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)])-3,6-dideoxy-3-oxoerythronolideB (Compound 92 in FIG. 8)

Treatment of 3,6-dideoxy-3-oxoerythronolide B (6 mg) as described inExample 9(A) gave5-O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)]-3,6-dideoxy-3-oxoerythronolideB (compound 90 in FIG. 8) in 44% yield. APCI-MS gives [M+H]+=600. Asecond product,5,11-bis-(O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)])-3,6-dideoxy-3-oxoerythronolideB (compound 92 in FIG. 8), was also isolated from this mixture in 26%yield; APCI-MS gives [M+H]+=815.

Example 12 Preparation of5-O-(1-β-(D)-desosaminyl)-3,6-dideoxy-3-oxoerythronolide B (Compound 91in FIG. 8) and of5,11-bis-O-(1-β-(D)-desosaminyl)-3,6-dideoxy-3-oxoerythronolide B(Compound 93 in FIG. 8)

Treatment of5-O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)]-3,6-dideoxy-3-oxoerythronolideB of Example 11 as described in Example 9(B) gave5-O-(1-β-(D)-desosaminyl)-3,6-dideoxy-3-oxoerythronolide B of Example 11(compound 91 in FIG. 8) in quantitative yield. APCI-MS gives [M+H]+=542.

Treatment of5,11-bis-(O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)])-3,6-dideoxy-3-oxoerythronolideB of Example 11 as described in Example 9(B) gave5,11-bis-O-(1-β-(D)-desosaminyl)-3,6-dideoxy-3-oxoerythronolide B(compound 93 in FIG. 8) in quantitative yield. APCI-MS gives [M+H]+=699.

Example 13 Preparation of2′-O-methoxycarbonyl-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin(Compound 83 in FIG. 8) and3,9-bis-(O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)])-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethonolide(Compound 84 in FIG. 8)

Treatment of (8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin(12 mg) according to the procedure of Example 9(A) yielded2′-O-methoxycarbonyl-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin(compound 82 in FIG. 8) (34%); APCI-MS gave [M+H]+=544. A secondproduct,3,9-bis-(O-[1-β-(2-O-methoxycarbonyl-(D)-desosaminyl)])-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethonolide(compound 84 in FIG. 8), was also isolated from this mixture (33%),APCI-MS gave [M+H]+=759.

Example 14 Preparation of(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin (Compound 83in FIG. 8) and of(8R,9S)-10-deoxy-8,9-dihydro-9-(1-β-(D)-desosaminyloxy)-8-methylmethymycin(Compound 85 in FIG. 8)

Treatment of2′-O-methoxycarbonyl-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycinof Example 13 as described in Example 9(B) gave(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin (compound 83in FIG. 8) in quantitative yield. APCI-MS gives [M+H]+=486.

Treatment of3,9-bis-(O-[1-β-(2-methoxycarbonyl-(D)-desosaminyl)])-(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethonolideof Example 13 as described in Example 9(B) gave(8R,9S)-10-deoxy-8,9-dihydro-9-hydroxy-8-methylmethymycin (compound 85in FIG. 8) in quantitative yield (elution from the C18 solid-phaseextraction cartridge was with 100% methanol). APCI-MS gives [M+H]+=643.

Example 15 Preparation of 14,15-dehydroerythromycin A (Compound 95 inFIG. 9)

A sample of 14,15-dehydro-6-deoxyerythronolide B (0.75 mg) from Example7 was dissolved in 0.6 mL of ethanol and diluted to 3 mL with sterilewater. This solution was used to overlay a 3 day old culture ofSaccharopolyspora erythraea WHM34 (eryA) grown on a 100 mm R2YE agarplate at 30° C. After drying, the plate was incubated at 30° C. for 4days. The agar was chopped and extracted 3 times with 100 mL portions of1% triethylamine in ethyl acetate. The extracts were combined andevaporated. The crude product was purified by preparative HPLC (C18reversed phase, water-acetonitrile gradient containing 1% acetic acid).Fractions were analyzed by mass spectrometry, and those containing pure14,15-dehydroerythromycin A (compound 95 in FIG. 9) were pooled,neutralized with triethylamine, and evaporated to a syrup. This wasdissolved in water and extracted 3 times with equal volumes of ethylacetate. The organic extracts were combined, washed once with saturatedaqueous NaHCO₃, dried over Na₂SO₄, filtered, and evaporated to yield0.15 mg of product. APCI-MS gives [M+H]+=733.

Example 16 Preparation of 14-oxo-8,8a-deoxyoleandolide (Compound 108)and 8,8a-deoxyoleandolide-14-carboxylic acid (compound 109) andDerivatives Thereof

These compounds can be prepared through ozonolysis of14,15-dehydro-6-deoxyerythonolide B (Compound 94 of FIG. 9).

A solution of compound 94 in methanol is cooled to −40° C., and ozone isbubbled into the solution until formation of I₂ is observed in a KIsolution attached to the outlet of the reaction vessel. Excess ozone ispurged from the solution by sparging with nitrogen gas, providing asolution of the ozonide of compound 94. Treatment of this solution withMe₂S will reduce the ozonide to the aldehyde, compound 108.

Alternatively, the ozonide can be oxidized by addition of H₂O₂ toprovide the corresponding carboxylic acid, compound 109.

Methods for converting the aldehyde to amines via reductive amination(e.g., using an amine and NaBH₃CN under mildly acidic conditions, orthrough formation of an oxime followed by catalytic hydrogenation) arewell known in the art. Similarly well known are methods for convertingthe carboxylic acid into esters or amides such as compound 110 (e.g.,through activation using a carbodiimide reagent in the presence of analcohol or an amine). Diamines in either procedure are used to producedimeric macrolides such as compounds 111 and 112. (See FIG. 6H)

Example 17 Diketide thioester Synthesis:(2S,3R)-3-hydroxy-2-methyl-4-pentenoic acid N-acetylcysteamine thioester

All diketide thioesters were synthesized by a common procedure.Illustrated here is the synthesis of(2S,3R)-3-hydroxy-2-methyl-4-pentenoic acid N-acetylcysteaminethioester. Enantioselective syn-aldol condensations were performedaccording to the procedure of D. A. Evans et al., J Am Chem Soc (1992)114:9434-9453. Subsequent manipulations followed the general proceduresof D. E. Cane et al., J Antibiotics (1995)48: 647-651.

The synthesis of[4S,3(2S,3R)]-4-benzyl-3-(3-hydroxy-2-methyl-4-pentenoyl)-2-oxazolidinoneby aldol condensation between (4S)-N-propionyl-4-benzyl-2-oxazolidinone(1.17 g, 5.0 mmol) and acrolein (0.4 mL, 11 mmol) was performed asdescribed by D. A. Evans et al., J Am Chem Soc (1992) 114:9434-9453,yielding 0.72 g of the adduct (50% yield) after chromatography onSiO2(2:1 hexane/ethyl acetate).

The aldol adduct was treated with t-butyldimethylsilyltrifluoromethanesulfonate (0.63 mL, 2.7 mmol) and 2,6-lutidine (0.35 mL,3 mmol) in THF at 0° C., yielding the O-silyl ether in quantitativeyield after chromatography (4.1 hexane/ethyl acetate).

A solution of the O-silyl ether in 20 mL of THF was cooled on ice, and2.8 mL of water was added followed by 0.61 mL of 50% H₂O₂. After 10 min,a solution of 215 mg of LiOH*H₂O in 2 mL of water was added. Thereaction was monitored by TLC, which revealed completion after 1 hour. Asolution of 1.25 g of sodium sulfite in 8 mL of water was added, andvolatiles were removed by rotary evaporation under reduced pressure. Theresulting aqueous mixture was extracted three times with 20 mL portionsof CH₂Cl₂, then acidified to pH 2 using 6N HCl and extracted 3 timeswith 50 mL portions of ethyl acetate. The ethyl acetate extracts werecombined, washed with brine, dried over Na₂SO₄, filtered, and evaporatedto provide the product acid as a colorless oil, 470 mg (70%).

The acid was dissolved in 10 mL of anhydrous dimethylformamide andcooled on ice. After addition of diphenylphosphorylazide (1.25 mL) andtriethylamine (1.06 mL), the mixture was stirred for 2 hrs on ice.

N-acetylcysteamine (1.5 mL) was added, and the mixture was stirredovernight at room temperature. After dilution with water, the mixturewas extracted 3 times with ethyl acetate. The extracts were combined,washed with brine, dried over Na₂SO₄, filtered, and evaporated toprovide the crude O-silyl thioester. Chromatography (1:1 hexane/ethylacetate) provided pure product (460 mg, 70%).

The O-silyl thioester (400 mg) was dissolved in 25 mL of acetonitrile,and 5 mL of water was added followed by 2 mL of 48% HF. After 2 hours,an additional 2 mL of 48% HF was added. After a total of 3.5 hours, thereaction was stopped by addition of sat. NaHCO₃ to neutral pH. Theproduct was extracted with 3 portions of ethyl acetate, and the combinedextracts were washed with brine, dried over Na₂SO₄, filtered, andevaporated to provide the desilylated thioester. Chromatography (Ethylacetate) gave 150 mg (56%) of pure(2S,3R)-3-hydroxy-2-methyl-4-pentenoic acid N-acetylcysteaminethioester, APCI-MC: [M+H]+=232. 1H-NMR (CDCl3): d 5.83, 1H, ddd(J=5.6,10.8,17.5); 5.33, 1H, ddd (J=1.6,1.6,16.9); 5.22, 1H, ddd(J=1.5,1.5,10.8); 4.45, 1H, m; 3.45, 2H, m, 3.04, 2H, m, 2.82, 1H, dq(J=4.3,6.8); 1.96, 3H, s; 1.22, 3H, d (J=6.8).

Other diketide thioesters were prepared by substitution of appropriatealdehydes in place of acrolein.

Example 18 Measurement of Antibacterial Activity

Antibacterial activity was determined using either disk diffusion assayswith Bacillus cereus as the test organism or by measurement of minimuminhibitory concentrations (MIC) in liquid culture against sensitive andresistant strains of Staphylococcus pneumoniae.

48 23 amino acids amino acid single linear peptide 1 Ala Thr Ala Cys ProLys Ser Ala Thr Lys Arg Ala Cys Pro Lys Ser 1 5 10 15 Ala Thr Lys ArgAla Cys Pro 20 20 amino acids amino acid single linear peptide 2 Lys SerAla Thr Ala Cys Pro Lys Ser Ala Thr Asp His Glu Arg Lys 1 5 10 15 ArgAla Cys Pro 20 20 amino acids amino acid single linear peptide 3 Lys SerAla Thr Lys Arg Ala Cys Pro Lys Ser Ala Thr Lys Arg Ala 1 5 10 15 CysPro Thr Glu 20 26 amino acids amino acid single linear peptide 4 Ala ThrAla Cys Pro Lys Ser Ala Thr Lys Arg Ala Cys Pro Lys Ser 1 5 10 15 AlaThr Lys Arg Ala Cys Pro Thr Thr Pro 20 25 24 base pairs nucleic acidsingle linear 5 GCGCAGCAGG GATCCGTCTT CGTC 24 24 base pairs nucleic acidsingle linear 6 CGCGTCTGGC TGCAGCCGAA GCCG 24 24 base pairs nucleic acidsingle linear 7 CCGGCCGAAT CTAGAGTGGG CGCG 24 24 base pairs nucleic acidsingle linear 8 TCCGACGGTG GATCCGTGTT CGTC 24 24 base pairs nucleic acidsingle linear 9 CGGTTCTGGC TGCAGCCGGA CCGC 24 24 base pairs nucleic acidsingle linear 10 ACGGAGAGCT CTAGAGACCG GCTG 24 24 base pairs nucleicacid single linear 11 GACGGGCGCG GATCCGTCTT CCTG 24 24 base pairsnucleic acid single linear 12 CGCTACTGGC TGCAGCCCGC CGCA 24 24 basepairs nucleic acid single linear 13 ACCGGCGAGT CTAGACAACG GCTC 24 24base pairs nucleic acid single linear 14 GCGCCGCGCG GATCCGTCCT GGTC 2424 base pairs nucleic acid single linear 15 CGCTTCTGGC TGCAGCCGCA CCGG24 24 base pairs nucleic acid single linear 16 GGGCCGAACT CTAGAGACCGGCTC 24 24 base pairs nucleic acid single linear 17 ACTCGCCGCGGATCCGCGAT GGTG 24 24 base pairs nucleic acid single linear 18CGGTACTGGC TGCAGATCCC CACC 24 24 base pairs nucleic acid single linear19 GAGGAGGGCT CTAGACTCGC CCAG 24 24 base pairs nucleic acid singlelinear 20 TCCGCCGGCG GATCCGTTTT CGTC 24 24 base pairs nucleic acidsingle linear 21 CGGTACTGGC TGCAGCCGGA GGTG 24 24 base pairs nucleicacid single linear 22 GTGGGGGCCT CTAGAGCGGT GCAG 24 23 base pairsnucleic acid single linear 23 CTGCAGGTCG ACTCTAGCCT GGT 23 27 base pairsnucleic acid single linear 24 TTTAGATCTG TGTTCGTCTT CCCGGGT 27 36 basepairs nucleic acid single linear 25 TTTCTGCAGC CAGTACCGCT GGTGCTGGAAGGCGTA 36 33 base pairs nucleic acid single linear 26 TTTGGATCCGCCTTCCTGTT CGACGGGCAA GGC 33 33 base pairs nucleic acid single linear 27TTTCTGCAGC CAGTAGGACT GGTGCTGGAA CGG 33 36 base pairs nucleic acidsingle linear 28 TTTCTGCAGG AGGGCACGGA CCGGGCGACT GCGGGT 36 36 basepairs nucleic acid single linear 29 TTTTCTAGAA CCGGCGGCAG CGGCCCGCCGAGCAAT 36 26 base pairs nucleic acid single linear 30 TTCTGCAGAGCGTGGACCGG GCGGCT 26 30 base pairs nucleic acid single linear 31TTTTCTAGAG TCACCGGTAG AGGCGGCCCT 30 30 base pairs nucleic acid singlelinear 32 TTTCTGCAGG GCGTGGACCG GGCGGCTGCC 30 30 base pairs nucleic acidsingle linear 33 TTTCTCGAGC ACCACGCCCG CAGCCTCACC 30 30 base pairsnucleic acid single linear 34 TTTCTCGAGG TCGGTCCGGA GGTCCAGGAT 30 30base pairs nucleic acid single linear 35 TTTTCTAGAA TCACCGGTAGAAGCAGCCCG 30 24 base pairs nucleic acid single linear 36 GAGCCCCAGCGGTACTGGCT GCAG 24 24 base pairs nucleic acid single linear 37TCTAGAGCGG TGCAGGCGGC CCCG 24 30 base pairs nucleic acid single linear38 TTTGGATCCG TTTTCGTCTT CCCAGGTCAG 30 30 base pairs nucleic acid singlelinear 39 TTTCTGCAGC CAGTACCGCT GGGGCTCGAA 30 30 base pairs nucleic acidsingle linear 40 TTTTCTAGAG CGGTGCAGGC GGCCCCGGCG 30 29 base pairsnucleic acid single linear 41 AAAATGCATC TATGAATTCC CTCCGCCCA 29 24 basepairs nucleic acid single linear 42 GAACACCAGC GCTTCTGGCT GCAG 24 24base pairs nucleic acid single linear 43 TCTAGAGACC GGCTCGCCGG TCGG 2421 base pairs nucleic acid single linear 44 AGTGCCTCCG ACGGTGGATC T 2124 base pairs nucleic acid single linear 45 CTGCAGCCGG ACCGCACCAC CCCT24 47 base pairs nucleic acid single linear 46 GCCGGACCGC ACCACCCCTCGTGACGGAGA ACCGGAGACG GAGAGCT 47 55 base pairs nucleic acid singlelinear 47 TGCAGCCGGA CCGCACCACC CCTCGTGACG GAGAACCGGA GACGGAGAGC TCTAG55 12 base pairs nucleic acid single linear cDNA 48 CTCACTAGTC AG 12

What is claimed is:
 1. A compound which is a polyketide or is an alteredform of said polyketide obtainable by treating said polyketide with aculture of S. erythraea, wherein said polyketide is selected from thegroup consisting of

wherein R is H or methyl.
 2. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 3. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 4. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 5. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 6. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 7. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 8. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 9. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 10. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 11. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 12. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 13. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 14. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 15. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 16. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 17. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 18. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 19. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 20. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 21. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 22. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 23. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 24. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 25. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 26. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 27. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 28. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 29. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 30. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 31. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 32. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 33. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 34. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 35. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 36. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 37. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 38. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 39. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 40. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 41. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 42. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 43. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 44. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 45. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 46. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 47. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 48. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 49. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 50. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 51. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 52. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.
 53. The compound of claim 1 wherein thepolyketide has the formula

wherein R is H or methyl.